Files

Ignacio Ballesteros 38b4e0b341 Fix index.md not being generated

- Generate index even when no .org files are found
- Don't halt CLI early when no org files - let pipeline complete
- Index will be empty but present, allowing Quartz to serve something

2026-02-22 11:45:56 +01:00

312 KiB

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Agent Shell Transcript

Agent: OpenCode Started: 2026-02-21 16:40:33 Working Directory: /home/ignaciobll/code/org-garden/

User (2026-02-21 16:40:33)

What does it need to be converted into a proper service, could be a nix service configuration, and other improvements for long running programs.

Tool Call [completed]: task

Tool: other Timestamp: 2026-02-21 16:42:01

task_id: ses_37f23cae7ffe0edPpg3vlYt4Sl (for resuming to continue this task if needed)

<task_result>
Now I have a complete picture of the project. Let me compile my analysis:

---

# OrgGarden Service Architecture Analysis

## Executive Summary

OrgGarden is an Elixir-based org-roam to static website publishing pipeline. It currently operates as a **CLI escript** with some supervisor infrastructure, but lacks several components needed for production-grade long-running service operation.

---

## 1. Current Architecture

### How It Runs Currently

| Mode | Entry Point | Behavior |
|------|-------------|----------|
| **serve** | `OrgGarden.CLI.handle_serve/1` | Starts supervisor tree, runs forever via `Process.sleep(:infinity)` |
| **build** | `OrgGarden.CLI.handle_build/1` | One-shot batch process, exits on completion |
| **export** | `OrgGarden.CLI.handle_export/1` | Batch export, optional watch mode with manual Watcher start |

**Key Files:**
- `/home/ignaciobll/code/org-garden/lib/org_garden/cli.ex` - Escript entry point
- `/home/ignaciobll/code/org-garden/lib/org_garden/application.ex` - Application callback
- `/home/ignaciobll/code/org-garden/mix.exs` - Configured as an escript (`main_module: OrgGarden.CLI`)

---

## 2. Process Supervision

### Current Supervisor Structure

OrgGarden.AppSupervisor (Application-level, :one_for_one) └── Finch (HTTP client pool)

OrgGarden.Supervisor (Dynamic, started by CLI, :one_for_all) ├── OrgGarden.Watcher (GenServer - file system watcher) └── OrgGarden.Quartz (GenServer - Node.js port wrapper)


### Issues Identified

| Issue | Location | Problem |
|-------|----------|---------|
| **Disconnected trees** | `application.ex` vs `supervisor.ex` | `OrgGarden.Supervisor` is started dynamically by CLI, not part of the application supervision tree |
| **No Registry** | - | Named processes (`name: __MODULE__`) prevent multiple instances |
| **Missing supervision** | `cli.ex:97,209` | Main process just sleeps forever (`Process.sleep(:infinity)`) - crash in CLI = orphaned children |
| **Export mode** | `cli.ex:200-207` | Watcher started outside supervisor when using `--watch` flag |

### Relevant Code

**Application.ex (line 7-12):**
```elixir
children = [
  {Finch, name: OrgGarden.Finch}
]
opts = [strategy: :one_for_one, name: OrgGarden.AppSupervisor]

Supervisor.ex (line 32-38):

children = [
  {OrgGarden.Watcher, ...},
  {OrgGarden.Quartz, ...}
]
Supervisor.init(children, strategy: :one_for_all)

3. State Management

Current State

Component	State Handling	Storage
Watcher	GenServer state (in-memory)	Transforms, pending debounce timers, paths
Quartz	GenServer state (in-memory)	Port reference, config
Citations	Transform state passed through	BibTeX entries (cached), Zotero availability flag

Issues

No persistent state - All state is in-memory only
No state recovery - Crash = lost state, full restart required
No ETS/Mnesia - No shared state between processes
Transform state per-request - BibTeX is reloaded on each batch run (but cached during watch mode)

4. Error Recovery

Current Behavior

Scenario	Handling	Location
Quartz exit	Stops GenServer with `{:stop, {:quartz_exit, status}, state}`	`quartz.ex:103-105`
File watcher stop	Stops GenServer with `{:stop, :watcher_stopped, state}`	`watcher.ex:99-101`
Export failure	Logs error, continues with other files	`watcher.ex:154-156`
Emacs export error	Returns `{:error, reason}`, caller handles	`export.ex:59-63`

What's Missing

No circuit breakers - Zotero/external service failures can cascade
No backoff/retry - Immediate restart attempts only (via supervisor)
No dead-letter handling - Failed files are logged but not queued for retry
No crash reporting - No integration with Sentry/Honeybadger/etc.

5. Graceful Shutdown

Current Implementation

Quartz terminate (line 109-117):

def terminate(_reason, %{port: port}) when is_port(port) do
  Port.close(port)
  :ok
rescue
  _ -> :ok
end

Watcher terminate (line 119-123):

def terminate(_reason, state) do
  OrgGarden.teardown_transforms(state.initialized_transforms)
  :ok
end

Issues

No shutdown timeout - Port.close/1 may not wait for Node.js to exit cleanly
No SIGTERM handling - Escript mode doesn't trap exits properly
No drain period - In-flight file processing may be interrupted
Pending debounce timers lost - Files changed just before shutdown may not be processed
No cleanup of temporary files - ox-hugo may leave intermediates

6. Configuration

Current Configuration Method

Environment Variables Only:

Variable	Purpose	Default
`QUARTZ_PATH`	Path to Quartz installation	Required for serve/build
`NODE_PATH`	Node.js executable	`"node"`
`BIBTEX_FILE`	BibTeX fallback file	None
`ZOTERO_URL`	Zotero Better BibTeX URL	`http://localhost:23119`
`CITATION_MODE`	silent/warn/strict	`warn`
`NOTES_DIR`	Source directory	Required (or CLI arg)
`OUTPUT_DIR`	Output directory	Current working directory

What's Missing

No config/*.exs files - Standard Elixir config not used at all
No runtime.exs - No Release-style configuration
No Application.get_env - All config via System.get_env directly
No validation - Missing required vars cause runtime crashes
No secrets management - Everything plain environment variables
No config reload - Changes require full restart

7. Logging/Observability

Current Logging

Logger Usage:

Logger.info/1 - General progress messages
Logger.warning/1 - Non-fatal issues (no BibTeX, Zotero unreachable)
Logger.error/1 - Failures (Quartz exit, export failures)
Logger.debug/1 - Detailed resolution tracing
IO.puts/1 - Direct console output (bypasses Logger)

Examples from code:

# watcher.ex:71
Logger.info("Watcher: monitoring #{notes_dir} for .org changes")

# quartz.ex:104
Logger.error("[quartz] Process exited with status #{status}")

# Direct IO (cli.ex:94-95)
IO.puts("==> Server running at http://localhost:#{opts[:port] || 8080}")

What's Missing

No structured logging - Plain strings only, no metadata
No log levels configurable - Hardcoded Logger calls
No telemetry - No :telemetry events for metrics
No tracing - No OpenTelemetry/distributed tracing
Mixed IO/Logger - Some output bypasses Logger entirely
No request IDs - No correlation for file processing events
No metrics - No processing time, file counts, error rates

8. Health Checks

Current Status

None exist. There are no health check endpoints, liveness probes, or readiness checks.

What Would Be Needed

Check Type	Purpose	Implementation Needed
Liveness	Is the process alive?	Simple HTTP endpoint
Readiness	Can it process files?	Check Quartz port alive, file watcher subscribed
Dependency	Are external services up?	Zotero probe, filesystem accessible
Deep health	Full system check	BibTeX loaded, Emacs available, Node.js working

Summary: What Exists vs What's Missing

Exists (Good Foundation)

Component	Status
GenServer-based workers	Watcher, Quartz
Basic supervisor	OrgGarden.Supervisor with :one_for_all
Terminate callbacks	Cleanup for port and transforms
HTTP client pooling	Finch in application tree
Transform lifecycle	init/apply/teardown pattern
File event debouncing	500ms debounce in Watcher

Missing for Production Service

Category	Gap
Supervision	Supervisor not in application tree; CLI process is unsupervised
Configuration	No config files; env vars only; no validation
Health checks	None
Metrics/Telemetry	None
Structured logging	Plain strings, mixed IO/Logger
Graceful shutdown	No SIGTERM trapping, no drain period
State persistence	All in-memory
Error recovery	No retries, no circuit breakers
Release support	Escript only, no Mix Release config

Recommendations for Service Conversion

Priority 1: Supervision Tree

Move OrgGarden.Supervisor into the Application supervision tree
Add dynamic supervisor for multiple watch directories
Replace Process.sleep(:infinity) with proper blocking

Priority 2: Configuration

Add config/config.exs and config/runtime.exs
Use Application.get_env/3 throughout
Add config validation at startup

Priority 3: Observability

Add :telemetry events for key operations
Implement structured logging with metadata
Create health check module with HTTP endpoint (via Plug/Bandit)

Priority 4: Release Support

Convert from escript to Mix Release
Add rel/env.sh.eex for environment configuration
Implement SIGTERM handler via :init.stop/0 </task_result>

## Agent (2026-02-21 16:42:03)

Based on the analysis, here's what's needed to make org-garden a proper long-running service:

## Critical Issues

### 1. **Supervision Tree Not Integrated**
- `OrgGarden.Supervisor` is started dynamically by CLI, not part of the Application tree
- CLI process just does `Process.sleep(:infinity)` - if it crashes, children are orphaned
- Export `--watch` mode starts Watcher outside any supervisor

### 2. **No Configuration System**
- All config via `System.get_env/1` directly, no `config/*.exs` files
- No validation of required values
- No runtime configuration support

### 3. **No Health Checks**
- No liveness/readiness probes
- No way to check if Quartz port or file watcher are healthy

### 4. **No Graceful Shutdown**
- No SIGTERM trapping (escript doesn't handle signals well)
- No drain period for in-flight file processing
- Pending debounce timers lost on shutdown

### 5. **No Observability**
- No `:telemetry` events for metrics
- Plain string logging, no structured metadata
- Mixed `IO.puts`/`Logger` usage

---

## For a Nix Service, You'd Need:

1. **NixOS module** (`module.nix`) with:
   - systemd service definition
   - User/group configuration
   - Environment variables from NixOS options
   - ExecReload for config changes
   - Proper restart policies

2. **Mix Release instead of escript** for:
   - Proper signal handling
   - Runtime configuration via `releases.exs`
   - Hot code upgrades (optional)

3. **Health check endpoint** (via Plug/Bandit) for systemd `Type=notify` or watchdog

---

## Quick Improvement Roadmap

| Priority | Item | Effort |
|----------|------|--------|
| 1 | Integrate supervisor into Application tree | Medium |
| 2 | Add `config/runtime.exs` | Low |
| 3 | Add `:telemetry` events | Medium |
| 4 | Convert to Mix Release | Medium |
| 5 | Add health check HTTP endpoint | Medium |
| 6 | Create NixOS module | Medium |
| 7 | Add structured logging | Low |

Want me to implement any of these improvements?

## User (2026-02-21 16:43:41)

Plan how to do these improvements



### Tool Call [failed]: todowrite

**Tool:** other
**Timestamp:** 2026-02-21 16:43:44

Tool execution aborted

## User (2026-02-21 16:43:50)

Plan how to do these improvements

## Agent (2026-02-21 16:43:52)

Let me read the key files to create a detailed implementation plan.

### Tool Call [completed]: read

**Tool:** read
**Timestamp:** 2026-02-21 16:43:53

/home/ignaciobll/code/org-garden/lib/org_garden/application.ex file 1: defmodule OrgGarden.Application do 2: @moduledoc false 3: use Application 4: 5: @impl true 6: def start(_type, _args) do 7: children = [ 8: {Finch, name: OrgGarden.Finch} 9: ] 10: 11: opts = [strategy: :one_for_one, name: OrgGarden.AppSupervisor] 12: Supervisor.start_link(children, opts) 13: end 14: end 15:

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### Tool Call [completed]: read

**Tool:** read
**Timestamp:** 2026-02-21 16:43:54

/home/ignaciobll/code/org-garden/lib/org_garden/supervisor.ex file 1: defmodule OrgGarden.Supervisor do 2: @moduledoc """ 3: Supervises development server components. 4: 5: Strategy: :one_for_all 6: If either child fails, restart both to ensure consistent state. 7: 8: Children: 9: 1. OrgGarden.Watcher - watches .org files for changes 10: 2. OrgGarden.Quartz - runs Quartz Node.js server 11: 12: ## Usage 13: 14: OrgGarden.Supervisor.start_link( 15: notes_dir: "/path/to/notes", 16: output_dir: "/path/to/output", 17: content_dir: "/path/to/output/content", 18: pipeline_opts: %{zotero_url: "...", ...}, 19: transforms: [OrgGarden.Transforms.Citations], 20: port: 8080, 21: ws_port: 3001 22: ) 23: """ 24: use Supervisor 25: 26: def start_link(opts) do 27: Supervisor.start_link(MODULE, opts, name: MODULE) 28: end 29: 30: @impl true 31: def init(opts) do 32: children = [ 33: {OrgGarden.Watcher, 34: Keyword.take(opts, [:notes_dir, :output_dir, :content_dir, :pipeline_opts, :transforms])}, 35: {OrgGarden.Quartz, Keyword.take(opts, [:content_dir, :port, :ws_port])} 36: ] 37: 38: Supervisor.init(children, strategy: :one_for_all) 39: end 40: end 41:

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### Tool Call [completed]: read

**Tool:** read
**Timestamp:** 2026-02-21 16:43:54

/home/ignaciobll/code/org-garden/lib/org_garden/cli.ex file 1: defmodule OrgGarden.CLI do 2: @moduledoc """ 3: Escript entry point for the org-garden pipeline. 4: 5: ## Commands 6: 7: org-garden serve [--port 8080] [--ws-port 3001] 8: org-garden build [--output ] 9: org-garden export [--watch] 10: 11: ### serve 12: Development server with watch + live reload. Starts both the org→md 13: watcher and Quartz in serve mode. 14: 15: ### build 16: One-shot build for CI/production. Exports org files, runs transforms, 17: then builds static site with Quartz. 18: 19: ### export 20: Just export org→md (current pipeline behavior). Use --watch for 21: incremental re-export on file changes. 22: 23: ## Arguments 24: 25: notes-dir Path to the directory containing .org notes (required). 26: Also accepts the NOTES_DIR env var. 27: 28: ## Options 29: 30: --output Output root directory (used as ox-hugo base dir). 31: Defaults to the OUTPUT_DIR env var, or the current 32: working directory. 33: --content-dir

Output directory for exported Markdown. Defaults to 34: <output>/content. 35: --port HTTP server port (default: 8080). Only for serve. 36: --ws-port WebSocket hot reload port (default: 3001). Only for serve. 37: --watch After initial batch, watch notes-dir for changes and 38: incrementally re-export affected files. Only for export. 39: 40: ## Environment Variables 41: 42: BIBTEX_FILE Path to a .bib file used as citation fallback. 43: ZOTERO_URL Zotero Better BibTeX base URL (default: http://localhost:23119). 44: CITATION_MODE silent | warn (default) | strict. 45: QUARTZ_PATH Path to quartz directory (required for serve/build). 46: NODE_PATH Node.js executable (default: node). 47: """ 48: 49: require Logger 50: 51: @transforms [OrgGarden.Transforms.Citations] 52: 53: def main(argv) do 54: Application.ensure_all_started(:org_garden) 55: 56: case argv do 57: ["serve" | rest] -> handle_serve(rest) 58: ["build" | rest] -> handle_build(rest) 59: ["export" | rest] -> handle_export(rest) 60: # Legacy: treat bare args as export command for backward compatibility 61: [_ | _] -> handle_export(argv) 62: _ -> abort("Usage: org-garden <serve|build|export> [options]") 63: end 64: end 65: 66: # --------------------------------------------------------------------------- 67: # Command: serve 68: # --------------------------------------------------------------------------- 69: 70: def handle_serve(argv) do 71: require_quartz_env() 72: {notes_dir, output_dir, content_dir, opts} = parse_serve_args(argv) 73: pipeline_opts = build_pipeline_opts() 74: 75: # Initial batch export 76: wipe(content_dir) 77: export_all(notes_dir, output_dir) 78: run_pipeline(content_dir, pipeline_opts) 79: generate_index(content_dir) 80: 81: IO.puts("==> Starting development server...") 82: 83: {:ok, _pid} = 84: OrgGarden.Supervisor.start_link( 85: notes_dir: notes_dir, 86: output_dir: output_dir, 87: content_dir: content_dir, 88: pipeline_opts: pipeline_opts, 89: transforms: @transforms, 90: port: opts[:port] || 8080, 91: ws_port: opts[:ws_port] || 3001 92: ) 93: 94: IO.puts("==> Server running at http://localhost:#{opts[:port] || 8080}") 95: IO.puts("==> Watching #{notes_dir} for changes (Ctrl+C to stop)") 96: 97: Process.sleep(:infinity) 98: end 99: 100: defp parse_serve_args(argv) do 101: {opts, positional, _invalid} = 102: OptionParser.parse(argv, 103: strict: [ 104: output: :string, 105: content_dir: :string, 106: port: :integer, 107: ws_port: :integer 108: ] 109: ) 110: 111: notes_dir = extract_notes_dir(positional, "serve") 112: output_dir = extract_output_dir(opts) 113: content_dir = extract_content_dir(opts, output_dir) 114: 115: {notes_dir, output_dir, content_dir, opts} 116: end 117: 118: # --------------------------------------------------------------------------- 119: # Command: build 120: # --------------------------------------------------------------------------- 121: 122: def handle_build(argv) do 123: quartz_path = require_quartz_env() 124: {notes_dir, output_dir, content_dir, _opts} = parse_build_args(argv) 125: pipeline_opts = build_pipeline_opts() 126: 127: # Full batch export 128: wipe(content_dir) 129: export_all(notes_dir, output_dir) 130: run_pipeline(content_dir, pipeline_opts) 131: generate_index(content_dir) 132: 133: node_path = System.get_env("NODE_PATH", "node") 134: 135: IO.puts("==> Building static site with Quartz...") 136: 137: {output, status} = 138: System.cmd( 139: node_path, 140: [ 141: Path.join(quartz_path, "quartz/bootstrap-cli.mjs"), 142: "build", 143: "--directory", 144: content_dir, 145: "--output", 146: Path.join(output_dir, "public") 147: ], 148: cd: quartz_path, 149: stderr_to_stdout: true 150: ) 151: 152: IO.puts(output) 153: 154: if status != 0 do 155: abort("Quartz build failed with status #{status}") 156: end 157: 158: IO.puts("==> Build complete. Output: #{Path.join(output_dir, "public")}") 159: end 160: 161: defp parse_build_args(argv) do 162: {opts, positional, _invalid} = 163: OptionParser.parse(argv, 164: strict: [output: :string, content_dir: :string] 165: ) 166: 167: notes_dir = extract_notes_dir(positional, "build") 168: output_dir = extract_output_dir(opts) 169: content_dir = extract_content_dir(opts, output_dir) 170: 171: {notes_dir, output_dir, content_dir, opts} 172: end 173: 174: # --------------------------------------------------------------------------- 175: # Command: export (original pipeline behavior) 176: # --------------------------------------------------------------------------- 177: 178: def handle_export(argv) do 179: {notes_dir, output_dir, content_dir, watch?} = parse_export_args(argv) 180: pipeline_opts = build_pipeline_opts() 181: 182: # Phase 1-4: full batch export 183: wipe(content_dir) 184: export_all(notes_dir, output_dir) 185: run_pipeline(content_dir, pipeline_opts) 186: generate_index(content_dir) 187: 188: md_count = 189: content_dir 190: |> Path.join("**/*.md") 191: |> Path.wildcard() 192: |> length() 193: 194: IO.puts("==> Done. #{md_count} markdown files in #{content_dir}") 195: 196: # Phase 5: optional watch mode 197: if watch? do 198: IO.puts("==> Watching #{notes_dir} for .org changes... (Ctrl+C to stop)") 199: 200: {:ok, _pid} = 201: OrgGarden.Watcher.start_link( 202: notes_dir: notes_dir, 203: output_dir: output_dir, 204: content_dir: content_dir, 205: pipeline_opts: pipeline_opts, 206: transforms: @transforms 207: ) 208: 209: Process.sleep(:infinity) 210: end 211: end 212: 213: defp parse_export_args(argv) do 214: {opts, positional, _invalid} = 215: OptionParser.parse(argv, 216: strict: [output: :string, content_dir: :string, watch: :boolean] 217: ) 218: 219: notes_dir = extract_notes_dir(positional, "export") 220: output_dir = extract_output_dir(opts) 221: content_dir = extract_content_dir(opts, output_dir) 222: watch? = Keyword.get(opts, :watch, false) 223: 224: {notes_dir, output_dir, content_dir, watch?} 225: end 226: 227: # --------------------------------------------------------------------------- 228: # Shared argument extraction 229: # --------------------------------------------------------------------------- 230: 231: defp extract_notes_dir(positional, command) do 232: notes_dir = 233: case positional do 234: [dir | _] -> 235: dir 236: 237: [] -> 238: System.get_env("NOTES_DIR") || 239: abort("Usage: org-garden #{command} [options]") 240: end 241: 242: notes_dir = Path.expand(notes_dir) 243: 244: unless File.dir?(notes_dir) do 245: abort("Error: notes directory does not exist: #{notes_dir}") 246: end 247: 248: notes_dir 249: end 250: 251: defp extract_output_dir(opts) do 252: (opts[:output] || System.get_env("OUTPUT_DIR") || File.cwd!()) 253: |> Path.expand() 254: end 255: 256: defp extract_content_dir(opts, output_dir) do 257: (opts[:content_dir] || Path.join(output_dir, "content")) 258: |> Path.expand() 259: end 260: 261: # --------------------------------------------------------------------------- 262: # Phase 1: Wipe content/ 263: # --------------------------------------------------------------------------- 264: 265: defp wipe(content_dir) do 266: IO.puts("==> Wiping #{content_dir}") 267: File.mkdir_p!(content_dir) 268: 269: content_dir 270: |> File.ls!() 271: |> Enum.reject(&(&1 == ".gitkeep")) 272: |> Enum.each(fn entry -> 273: Path.join(content_dir, entry) |> File.rm_rf!() 274: end) 275: end 276: 277: # --------------------------------------------------------------------------- 278: # Phase 2: Export org files via Emacs + ox-hugo 279: # --------------------------------------------------------------------------- 280: 281: defp export_all(notes_dir, output_dir) do 282: IO.puts("==> Exporting org files from #{notes_dir}") 283: 284: case OrgGarden.Export.export_all(notes_dir, output_dir) do 285: {:ok, 0} -> 286: IO.puts("No .org files found in #{notes_dir}") 287: System.halt(0) 288: 289: {:ok, count} -> 290: IO.puts(" exported #{count} file(s)") 291: 292: {:error, failures} -> 293: IO.puts(:stderr, "\nFailed to export #{length(failures)} file(s):") 294: 295: Enum.each(failures, fn {f, {:error, reason}} -> 296: IO.puts(:stderr, " #{f}: #{inspect(reason)}") 297: end) 298: 299: System.halt(1) 300: end 301: end 302: 303: # --------------------------------------------------------------------------- 304: # Phase 3: Markdown transformation pipeline 305: # --------------------------------------------------------------------------- 306: 307: defp run_pipeline(content_dir, pipeline_opts) do 308: IO.puts("==> Running markdown pipeline") 309: 310: {:ok, stats} = OrgGarden.run(content_dir, @transforms, pipeline_opts) 311: 312: Enum.each(stats, fn {mod, count} -> 313: IO.puts(" #{inspect(mod)}: #{count} file(s) modified") 314: end) 315: end 316: 317: # --------------------------------------------------------------------------- 318: # Phase 4: Generate default index.md if none was exported 319: # --------------------------------------------------------------------------- 320: 321: defp generate_index(content_dir) do 322: IO.puts("==> Generating index") 323: OrgGarden.Index.generate(content_dir) 324: end 325: 326: # --------------------------------------------------------------------------- 327: # Helpers 328: # --------------------------------------------------------------------------- 329: 330: defp require_quartz_env do 331: case System.get_env("QUARTZ_PATH") do 332: nil -> 333: abort(""" 334: Error: QUARTZ_PATH environment variable not set. 335: 336: The 'serve' and 'build' commands require Quartz to be available. 337: 338: Use the wrapper scripts that set up the environment: 339: nix run .#notes -- # for serve 340: nix run .#build -- # for build 341: 342: Or set QUARTZ_PATH manually to point to a quartz-org-roam checkout 343: with node_modules installed. 344: 345: For export-only mode (no Quartz), use: 346: org-garden export [--watch] 347: """) 348: 349: path -> 350: unless File.exists?(Path.join(path, "quartz/bootstrap-cli.mjs")) do 351: abort("Error: QUARTZ_PATH=#{path} does not contain quartz/bootstrap-cli.mjs") 352: end 353: 354: path 355: end 356: end 357: 358: defp build_pipeline_opts do 359: %{ 360: zotero_url: System.get_env("ZOTERO_URL", "http://localhost:23119"), 361: bibtex_file: System.get_env("BIBTEX_FILE"), 362: citation_mode: 363: case System.get_env("CITATION_MODE", "warn") do 364: "silent" -> :silent 365: "strict" -> :strict 366: _ -> :warn 367: end 368: } 369: end 370: 371: defp abort(message) do 372: IO.puts(:stderr, message) 373: System.halt(1) 374: end 375: end 376:

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### Tool Call [completed]: read

**Tool:** read
**Timestamp:** 2026-02-21 16:43:54

/home/ignaciobll/code/org-garden/mix.exs file 1: defmodule OrgGarden.MixProject do 2: use Mix.Project 3: 4: def project do 5: [ 6: app: :org_garden, 7: version: "0.1.0", 8: elixir: "> 1.17", 9: start_permanent: Mix.env() == :prod, 10: deps: deps(), 11: escript: escript() 12: ] 13: end 14: 15: def application do 16: [ 17: extra_applications: [:logger], 18: mod: {OrgGarden.Application, []} 19: ] 20: end 21: 22: defp escript do 23: [main_module: OrgGarden.CLI] 24: end 25: 26: defp deps do 27: [ 28: {:finch, "> 0.19"}, 29: {:req, "~~> 0.5"}, 30: {:jason, "~~> 1.4"}, 31: {:file_system, "~> 1.0"} 32: ] 33: end 34: end 35:

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**Timestamp:** 2026-02-21 16:43:57

/home/ignaciobll/code/org-garden/lib/org_garden/watcher.ex file 1: defmodule OrgGarden.Watcher do 2: @moduledoc """ 3: File-watching GenServer that detects .org file changes and triggers 4: incremental export + transform for only the affected files. 5: 6: Uses the file_system package (inotify on Linux, fsevents on macOS) 7: to watch the notes directory. Events are debounced per-file (500ms) 8: to coalesce rapid writes (e.g., Emacs auto-save). 9: 10: ## Lifecycle 11: 12: Started dynamically by OrgGarden.CLI after the initial batch export. 13: Transforms are initialized once at startup and reused across all 14: incremental rebuilds to avoid repeated Zotero probes and BibTeX loads. 15: 16: ## Usage 17: 18: OrgGarden.Watcher.start_link( 19: notes_dir: "/path/to/notes", 20: output_dir: "/path/to/output", 21: content_dir: "/path/to/output/content", 22: pipeline_opts: %{zotero_url: "...", ...}, 23: transforms: [OrgGarden.Transforms.Citations] 24: ) 25: """ 26: 27: use GenServer 28: 29: require Logger 30: 31: @debounce_ms 500 32: 33: # ------------------------------------------------------------------- 34: # Client API 35: # ------------------------------------------------------------------- 36: 37: @doc """ 38: Start the watcher as a linked process. 39: 40: ## Options 41: 42: * :notes_dir — directory to watch for .org changes (required) 43: * :output_dir — ox-hugo base dir (required) 44: * :content_dir — directory where .md files are written (required) 45: * :pipeline_opts — opts map passed to transforms (required) 46: * :transforms — list of transform modules (default: [OrgGarden.Transforms.Citations]) 47: """ 48: def start_link(opts) do 49: GenServer.start_link(MODULE, opts, name: MODULE) 50: end 51: 52: # ------------------------------------------------------------------- 53: # GenServer callbacks 54: # ------------------------------------------------------------------- 55: 56: @impl true 57: def init(opts) do 58: notes_dir = Keyword.fetch!(opts, :notes_dir) 59: output_dir = Keyword.fetch!(opts, :output_dir) 60: content_dir = Keyword.fetch!(opts, :content_dir) 61: pipeline_opts = Keyword.fetch!(opts, :pipeline_opts) 62: transforms = Keyword.get(opts, :transforms, [OrgGarden.Transforms.Citations]) 63: 64: # Initialize transforms once — reused for all incremental rebuilds 65: initialized_transforms = OrgGarden.init_transforms(transforms, pipeline_opts) 66: 67: # Start the file system watcher 68: {:ok, watcher_pid} = FileSystem.start_link(dirs: [notes_dir], recursive: true) 69: FileSystem.subscribe(watcher_pid) 70: 71: Logger.info("Watcher: monitoring #{notes_dir} for .org changes") 72: 73: {:ok, 74: %{ 75: notes_dir: notes_dir, 76: output_dir: output_dir, 77: content_dir: content_dir, 78: pipeline_opts: pipeline_opts, 79: watcher_pid: watcher_pid, 80: initialized_transforms: initialized_transforms, 81: pending: %{} 82: }} 83: end 84: 85: @impl true 86: def handle_info({:file_event, _pid, {path, events}}, state) do 87: path = to_string(path) 88: 89: if org_file?(path) and not temporary_file?(path) do 90: event_type = classify_events(events) 91: Logger.debug("Watcher: #{event_type} event for #{path}") 92: {:noreply, schedule_debounce(path, event_type, state)} 93: else 94: {:noreply, state} 95: end 96: end 97: 98: @impl true 99: def handle_info({:file_event, _pid, :stop}, state) do 100: Logger.warning("Watcher: file system monitor stopped unexpectedly") 101: {:stop, :watcher_stopped, state} 102: end 103: 104: @impl true 105: def handle_info({:debounced, path, event_type}, state) do 106: state = %{state | pending: Map.delete(state.pending, path)} 107: 108: case event_type do 109: :deleted -> 110: handle_delete(path, state) 111: 112: _created_or_modified -> 113: handle_change(path, state) 114: end 115: 116: {:noreply, state} 117: end 118: 119: @impl true 120: def terminate(_reason, state) do 121: OrgGarden.teardown_transforms(state.initialized_transforms) 122: :ok 123: end 124: 125: # ------------------------------------------------------------------- 126: # Event handling 127: # ------------------------------------------------------------------- 128: 129: defp handle_change(orgfile, state) do 130: %{ 131: notes_dir: notes_dir, 132: output_dir: output_dir, 133: content_dir: content_dir, 134: pipeline_opts: pipeline_opts, 135: initialized_transforms: initialized_transforms 136: } = state 137: 138: md_path = OrgGarden.Export.expected_md_path(orgfile, notes_dir, content_dir) 139: IO.puts("==> Changed: #{Path.relative_to(orgfile, notes_dir)}") 140: 141: case OrgGarden.Export.export_file(orgfile, notes_dir, output_dir) do 142: {:ok, _} -> 143: IO.puts(" exported: #{Path.relative_to(md_path, content_dir)}") 144: 145: {:ok, stats} = OrgGarden.run_on_files_with([md_path], initialized_transforms, pipeline_opts) 146: 147: Enum.each(stats, fn {mod, count} -> 148: if count > 0, do: IO.puts(" #{inspect(mod)}: #{count} file(s) modified") 149: end) 150: 151: regenerate_index(content_dir) 152: IO.puts("==> Done") 153: 154: {:error, reason} -> 155: Logger.error("Watcher: export failed for #{orgfile}: #{inspect(reason)}") 156: end 157: end 158: 159: defp handle_delete(orgfile, state) do 160: %{notes_dir: notes_dir, content_dir: content_dir} = state 161: 162: md_path = OrgGarden.Export.expected_md_path(orgfile, notes_dir, content_dir) 163: IO.puts("==> Deleted: #{Path.relative_to(orgfile, notes_dir)}") 164: 165: if File.exists?(md_path) do 166: File.rm!(md_path) 167: IO.puts(" removed: #{Path.relative_to(md_path, content_dir)}") 168: 169: # Clean up empty parent directories left behind 170: cleanup_empty_dirs(Path.dirname(md_path), content_dir) 171: end 172: 173: regenerate_index(content_dir) 174: IO.puts("==> Done") 175: end 176: 177: # ------------------------------------------------------------------- 178: # Index generation 179: # ------------------------------------------------------------------- 180: 181: defp regenerate_index(content_dir) do 182: OrgGarden.Index.regenerate(content_dir) 183: end 184: 185: # ------------------------------------------------------------------- 186: # Helpers 187: # ------------------------------------------------------------------- 188: 189: defp schedule_debounce(path, event_type, state) do 190: # Cancel any existing timer for this path 191: case Map.get(state.pending, path) do 192: nil -> :ok 193: old_ref -> Process.cancel_timer(old_ref) 194: end 195: 196: ref = Process.send_after(self(), {:debounced, path, event_type}, @debounce_ms) 197: %{state | pending: Map.put(state.pending, path, ref)} 198: end 199: 200: defp org_file?(path), do: String.ends_with?(path, ".org") 201: 202: defp temporary_file?(path) do 203: basename = Path.basename(path) 204: # Emacs creates temp files like .#file.org and #file.org# 205: String.starts_with?(basename, ".#") or 206: (String.starts_with?(basename, "#") and String.ends_with?(basename, "#")) 207: end 208: 209: defp classify_events(events) do 210: cond do 211: :removed in events or :deleted in events -> :deleted 212: :created in events -> :created 213: :modified in events or :changed in events -> :modified 214: # renamed can mean created or deleted depending on context; 215: # if the file exists it was renamed into the watched dir 216: :renamed in events -> :modified 217: true -> :modified 218: end 219: end 220: 221: defp cleanup_empty_dirs(dir, stop_at) do 222: dir = Path.expand(dir) 223: stop_at = Path.expand(stop_at) 224: 225: if dir != stop_at and File.dir?(dir) do 226: case File.ls!(dir) do 227: [] -> 228: File.rmdir!(dir) 229: cleanup_empty_dirs(Path.dirname(dir), stop_at) 230: 231: _ -> 232: :ok 233: end 234: end 235: end 236: end 237:

(End of file - total 237 lines)



### Tool Call [completed]: read

**Tool:** read
**Timestamp:** 2026-02-21 16:43:58

/home/ignaciobll/code/org-garden/lib/org_garden/quartz.ex file 1: defmodule OrgGarden.Quartz do 2: @moduledoc """ 3: Manages Quartz Node.js process as an Erlang Port. 4: 5: Required environment: 6: - QUARTZ_PATH: path to quartz repo (with node_modules) 7: - NODE_PATH: path to node executable (default: "node") 8: 9: Starts Quartz in serve mode (npx quartz build --serve) and forwards 10: all stdout/stderr output to the Logger with a [quartz] prefix. 11: 12: If Quartz exits, this GenServer will stop, which triggers the supervisor 13: to restart the entire supervision tree (strategy: :one_for_all). 14: """ 15: use GenServer 16: 17: require Logger 18: 19: defstruct [:port, :quartz_path, :content_dir, :http_port, :ws_port] 20: 21: # ------------------------------------------------------------------- 22: # Client API 23: # ------------------------------------------------------------------- 24: 25: @doc """ 26: Start the Quartz process as a linked GenServer. 27: 28: ## Options 29: 30: * :content_dir — directory where markdown files are located (required) 31: * :port — HTTP server port (default: 8080) 32: * :ws_port — WebSocket hot reload port (default: 3001) 33: """ 34: def start_link(opts) do 35: GenServer.start_link(MODULE, opts, name: MODULE) 36: end 37: 38: # ------------------------------------------------------------------- 39: # GenServer callbacks 40: # ------------------------------------------------------------------- 41: 42: @impl true 43: def init(opts) do 44: quartz_path = 45: System.get_env("QUARTZ_PATH") || 46: raise "QUARTZ_PATH environment variable not set" 47: 48: node_path = System.get_env("NODE_PATH", "node") 49: 50: content_dir = Keyword.fetch!(opts, :content_dir) 51: http_port = Keyword.get(opts, :port, 8080) 52: ws_port = Keyword.get(opts, :ws_port, 3001) 53: 54: cli_path = Path.join(quartz_path, "quartz/bootstrap-cli.mjs") 55: 56: unless File.exists?(cli_path) do 57: raise "Quartz CLI not found at #{cli_path}. Check QUARTZ_PATH." 58: end 59: 60: args = [ 61: cli_path, 62: "build", 63: "--serve", 64: "--directory", content_dir, 65: "--port", to_string(http_port), 66: "--wsPort", to_string(ws_port) 67: ] 68: 69: Logger.info("[quartz] Starting: #{node_path} #{Enum.join(args, " ")}") 70: Logger.info("[quartz] Working directory: #{quartz_path}") 71: 72: port = 73: Port.open({:spawn_executable, node_path}, [ 74: :binary, 75: :exit_status, 76: :stderr_to_stdout, 77: args: args, 78: cd: quartz_path, 79: env: [{~c"NODE_NO_WARNINGS", ~c"1"}] 80: ]) 81: 82: state = %MODULE{ 83: port: port, 84: quartz_path: quartz_path, 85: content_dir: content_dir, 86: http_port: http_port, 87: ws_port: ws_port 88: } 89: 90: {:ok, state} 91: end 92: 93: @impl true 94: def handle_info({port, {:data, data}}, %{port: port} = state) do 95: data 96: |> String.split("\n", trim: true) 97: |> Enum.each(&Logger.info("[quartz] #{&1}")) 98: 99: {:noreply, state} 100: end 101: 102: @impl true 103: def handle_info({port, {:exit_status, status}}, %{port: port} = state) do 104: Logger.error("[quartz] Process exited with status #{status}") 105: {:stop, {:quartz_exit, status}, state} 106: end 107: 108: @impl true 109: def terminate(_reason, %{port: port}) when is_port(port) do 110: # Attempt graceful shutdown 111: Port.close(port) 112: :ok 113: rescue 114: _ -> :ok 115: end 116: 117: def terminate(_reason, _state), do: :ok 118: end 119:

(End of file - total 119 lines)



### Tool Call [completed]: read

**Tool:** read
**Timestamp:** 2026-02-21 16:43:58

/home/ignaciobll/code/org-garden/flake.nix file 1: { 2: description = "Org-garden — org-roam to website publishing pipeline"; 3: 4: inputs = { 5: nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable"; 6: flake-utils.url = "github:numtide/flake-utils"; 7: }; 8: 9: outputs = { self, nixpkgs, flake-utils }: 10: flake-utils.lib.eachDefaultSystem (system: 11: let 12: pkgs = import nixpkgs { inherit system; }; 13: fs = pkgs.lib.fileset; 14: 15: # ========================================================================= 16: # Emacs with ox-hugo 17: # ========================================================================= 18: # Needed at runtime by the escript (export calls emacs --batch with ox-hugo) 19: emacsWithOxHugo = (pkgs.emacsPackagesFor pkgs.emacs-nox).emacsWithPackages 20: (epkgs: [ epkgs.ox-hugo ]); 21: 22: # ========================================================================= 23: # Elixir Pipeline 24: # ========================================================================= 25: 26: # Pre-fetched Hex/Mix dependencies 27: mixDeps = pkgs.beamPackages.fetchMixDeps { 28: pname = "org-garden-mix-deps"; 29: version = "0.1.0"; 30: src = fs.toSource { 31: root = ./.; 32: fileset = fs.unions [ 33: ./mix.exs 34: ./mix.lock 35: ]; 36: }; 37: sha256 = "sha256-si7JAomY1HZ33m6ihUJP5i6PO39CE1clYvuMtn0CbPU="; 38: }; 39: 40: # Compiled org-garden escript 41: orgGardenEscript = pkgs.beamPackages.mixRelease { 42: pname = "org-garden"; 43: version = "0.1.0"; 44: src = fs.toSource { 45: root = ./.; 46: fileset = fs.unions [ 47: ./mix.exs 48: ./mix.lock 49: ./lib 50: ]; 51: }; 52: escriptBinName = "org_garden"; 53: mixFodDeps = mixDeps; 54: stripDebug = true; 55: }; 56: 57: # ========================================================================= 58: # Quartz (fetched from upstream, patched) 59: # ========================================================================= 60: 61: # Pin to specific upstream commit 62: quartzVersion = "4.5.2"; 63: quartzRev = "ec00a40aefca73596ab76e3ebe3a8e1129b43688"; 64: 65: # Fetch upstream Quartz source 66: quartzSrc = pkgs.fetchFromGitHub { 67: owner = "jackyzha0"; 68: repo = "quartz"; 69: rev = quartzRev; 70: hash = "sha256-HdtQB5+SRWiypOvAJuJa3Nodl4JHehp2Mz6Rj5gOG0w="; 71: }; 72: 73: # Apply our patches to Quartz 74: quartzPatched = pkgs.runCommand "quartz-patched-${quartzVersion}" { 75: src = quartzSrc; 76: } '' 77: cp -r $src $out 78: chmod -R u+w $out 79: cd $out 80: patch -p1 < ${./patches/01-glob-gitignore.patch} 81: patch -p1 < ${./patches/02-build-gitignore.patch} 82: patch -p1 < ${./patches/03-static-hugo.patch} 83: patch -p1 < ${./patches/04-oxhugofm-figure.patch} 84: ''; 85: 86: # Pre-fetch Quartz npm dependencies 87: quartzDeps = pkgs.buildNpmPackage { 88: pname = "org-garden-quartz-deps"; 89: version = quartzVersion; 90: src = quartzPatched; 91: npmDepsHash = "sha256-7u+VlIx44B3/ivM9vLMIOn+e4TL4eS6B682vhS+Ikb4="; 92: dontBuild = true; 93: installPhase = '' 94: mkdir -p $out 95: cp -r node_modules $out/node_modules 96: ''; 97: }; 98: 99: # ========================================================================= 100: # Combined Application 101: # ========================================================================= 102: 103: # Wrapped org-garden with Quartz bundled 104: orgGardenApp = pkgs.writeShellApplication { 105: name = "org-garden"; 106: runtimeInputs = [ emacsWithOxHugo pkgs.inotify-tools pkgs.nodejs_22 ]; 107: text = '' 108: # Set up Quartz working directory 109: QUARTZ_WORK=$(mktemp -d) 110: trap 'rm -rf "$QUARTZ_WORK"' EXIT 111: 112: # Copy patched Quartz source 113: cp -r ${quartzPatched}/. "$QUARTZ_WORK/" 114: chmod -R u+w "$QUARTZ_WORK" 115: 116: # Copy default config files 117: cp ${./quartz-config/quartz.config.ts} "$QUARTZ_WORK/" 118: cp ${./quartz-config/quartz.layout.ts} "$QUARTZ_WORK/" 119: cp ${./quartz-config/globals.d.ts} "$QUARTZ_WORK/" 120: cp ${./quartz-config/index.d.ts} "$QUARTZ_WORK/" 121: 122: # Link pre-built node_modules 123: ln -s ${quartzDeps}/node_modules "$QUARTZ_WORK/node_modules" 124: 125: export QUARTZ_PATH="$QUARTZ_WORK" 126: export NODE_PATH="${pkgs.nodejs_22}/bin/node" 127: 128: exec ${orgGardenEscript}/bin/org_garden "$@" 129: ''; 130: }; 131: 132: in 133: { 134: packages.default = orgGardenApp; 135: packages.escript = orgGardenEscript; 136: packages.quartz-patched = quartzPatched; 137: 138: devShells.default = pkgs.mkShell { 139: buildInputs = [ 140: pkgs.elixir 141: pkgs.inotify-tools 142: emacsWithOxHugo 143: pkgs.nodejs_22 144: ]; 145: }; 146: }); 147: } 148:

(End of file - total 148 lines)

## Agent (2026-02-21 16:44:01)

Now I have a complete picture of the codebase. Let me create a comprehensive implementation plan.

---

# Implementation Plan: Converting org-garden to a Production Service

## Overview

The goal is to transform org-garden from an escript CLI into a proper long-running Elixir service that can be deployed as a NixOS systemd service with proper supervision, configuration, health checks, and observability.

---

## Phase 1: Supervision Tree Integration

**Goal:** Ensure all processes are properly supervised and the application can run without `Process.sleep(:infinity)`.

### 1.1 Refactor Application Module

**File:** `lib/org_garden/application.ex`

- Add `OrgGarden.Supervisor` as a child of the Application supervisor
- Use a `DynamicSupervisor` to allow starting/stopping service modes dynamically
- Add a `Registry` for named process lookup (enables multiple instances if needed)

OrgGarden.AppSupervisor (:one_for_one) ├── Finch (HTTP client pool) ├── Registry (process registry) └── DynamicSupervisor (for serve/export workers) ├── OrgGarden.Supervisor (when serve mode) │ ├── Watcher │ └── Quartz └── OrgGarden.Watcher (when export --watch mode)


### 1.2 Create Server Module

**New file:** `lib/org_garden/server.ex`

- Encapsulate the "serve" mode startup logic
- Provide `start/1`, `stop/0` API
- Handles initial export, then starts supervised Watcher + Quartz
- Replaces `Process.sleep(:infinity)` with proper blocking via GenServer

### 1.3 Update CLI

**File:** `lib/org_garden/cli.ex`

- Remove `Process.sleep(:infinity)` calls
- Use the new `OrgGarden.Server.start/1` which blocks properly
- Handle SIGTERM via `:init.stop/0` or System signals

**Estimated effort:** Medium (2-3 hours)

---

## Phase 2: Configuration System

**Goal:** Replace scattered `System.get_env/1` calls with proper Elixir configuration.

### 2.1 Create Config Files

**New files:**
- `config/config.exs` — Base configuration with defaults
- `config/runtime.exs` — Runtime config from environment variables (Release-style)

### 2.2 Create Config Module

**New file:** `lib/org_garden/config.ex`

- Centralized configuration access via `OrgGarden.Config.get/1`
- Validation at startup (fail fast if required config missing)
- Type coercion (e.g., string ports to integers)

### 2.3 Update All Modules

Replace direct `System.get_env/1` calls in:
- `lib/org_garden/cli.ex`
- `lib/org_garden/quartz.ex`
- `lib/org_garden/transforms/citations.ex`

**Estimated effort:** Low-Medium (1-2 hours)

---

## Phase 3: Health Checks

**Goal:** Add HTTP health endpoint for systemd/kubernetes health probes.

### 3.1 Add HTTP Dependencies

**File:** `mix.exs`

Add minimal HTTP server:
```elixir
{:bandit, "~> 1.0"},
{:plug, "~> 1.15"}

3.2 Create Health Module

New file: lib/org_garden/health.ex

Endpoints:

GET /health/live — Process alive (always 200)
GET /health/ready — Dependencies ready (check Quartz port, Watcher subscribed)
GET /health — Combined status JSON

3.3 Add to Supervision Tree

Start Bandit under OrgGarden.AppSupervisor on a configurable port (default: 9090).

Estimated effort: Medium (2 hours)

Phase 4: Graceful Shutdown

Goal: Proper cleanup when service stops.

4.1 Add Signal Handling

File: lib/org_garden/application.ex

Trap exits with Process.flag(:trap_exit, true)
Handle :sigterm to initiate graceful shutdown

4.2 Improve Quartz Termination

File: lib/org_garden/quartz.ex

Send SIGTERM to Node.js process instead of just Port.close/1
Wait for graceful exit with timeout
Force kill if timeout exceeded

4.3 Add Drain Period

File: lib/org_garden/watcher.ex

On shutdown, flush pending debounce timers
Wait for in-flight file processing to complete
Configurable drain timeout

Estimated effort: Medium (2 hours)

Phase 5: Observability

Goal: Add telemetry events and structured logging.

5.1 Add Telemetry Events

New file: lib/org_garden/telemetry.ex

Events:

[:org_garden, :export, :start | :stop | :exception]
[:org_garden, :transform, :start | :stop]
[:org_garden, :watcher, :file_changed]
[:org_garden, :quartz, :request]

5.2 Structured Logging

File: lib/org_garden/application.ex

Configure Logger with metadata:

config :logger, :console,
  format: "$time $metadata[$level] $message\n",
  metadata: [:file, :module, :request_id]

5.3 Replace IO.puts with Logger

Files: cli.ex, watcher.ex, quartz.ex

Replace all IO.puts/1 with Logger.info/1
Add metadata where appropriate

Estimated effort: Medium (2-3 hours)

Phase 6: Mix Release Support

Goal: Build as a proper OTP release instead of escript.

6.1 Add Release Configuration

File: mix.exs

def project do
  [
    ...
    releases: [
      org_garden: [
        include_executables_for: [:unix],
        applications: [runtime_tools: :permanent]
      ]
    ]
  ]
end

6.2 Create Release Scripts

New files:

rel/env.sh.eex — Environment setup
rel/vm.args.eex — BEAM VM arguments

6.3 Update flake.nix

Replace mixRelease escript build with proper release:

orgGardenRelease = pkgs.beamPackages.mixRelease {
  ...
  buildPhase = "mix release --overwrite";
};

Estimated effort: Medium (2 hours)

Phase 7: NixOS Module

Goal: Provide a NixOS module for easy deployment.

7.1 Create NixOS Module

New file: nix/module.nix

{ config, lib, pkgs, ... }:
{
  options.services.org-garden = {
    enable = lib.mkEnableOption "org-garden service";
    
    notesDir = lib.mkOption {
      type = lib.types.path;
      description = "Path to org-roam notes directory";
    };
    
    outputDir = lib.mkOption {
      type = lib.types.path;
      default = "/var/lib/org-garden";
    };
    
    port = lib.mkOption {
      type = lib.types.port;
      default = 8080;
    };
    
    healthPort = lib.mkOption {
      type = lib.types.port;
      default = 9090;
    };
    
    # ... more options
  };

  config = lib.mkIf config.services.org-garden.enable {
    systemd.services.org-garden = {
      description = "Org-Garden Publishing Service";
      wantedBy = [ "multi-user.target" ];
      after = [ "network.target" ];
      
      serviceConfig = {
        Type = "exec";
        ExecStart = "${orgGardenApp}/bin/org-garden serve ...";
        Restart = "on-failure";
        RestartSec = 5;
        
        # Hardening
        DynamicUser = true;
        StateDirectory = "org-garden";
        ProtectSystem = "strict";
        ProtectHome = true;
        NoNewPrivileges = true;
      };
      
      environment = {
        NOTES_DIR = config.services.org-garden.notesDir;
        # ...
      };
    };
  };
}

7.2 Add to Flake Outputs

File: flake.nix

outputs = {
  ...
  nixosModules.default = import ./nix/module.nix;
};

Estimated effort: Medium (2-3 hours)

Implementation Order

Phase	Dependency	Effort	Priority
1. Supervision Tree	None	Medium	Critical
2. Configuration	None	Low-Medium	High
4. Graceful Shutdown	Phase 1	Medium	High
3. Health Checks	Phase 1, 2	Medium	Medium
5. Observability	Phase 2	Medium	Medium
6. Mix Release	Phase 1-5	Medium	Medium
7. NixOS Module	Phase 6	Medium	Low

Recommended order: 1 → 2 → 4 → 3 → 5 → 6 → 7

Total estimated effort: 14-18 hours

Questions Before Implementation

Health check port: Should it be separate from the Quartz HTTP port, or should we add routes to Quartz itself?
Multiple instances: Do you need to run multiple org-garden instances (different notes dirs) on the same machine? This affects Registry design.
Metrics backend: Do you want to add Prometheus metrics export, or just telemetry events for now?
Backwards compatibility: Should the escript CLI still work, or can we fully migrate to Mix Release?
NixOS module scope: Should it support both serve and build modes, or just serve as a long-running service?

User (2026-02-21 16:45:45)

In the case of the CLI script, a mix release approach will allow us to run it standalone also?

Agent (2026-02-21 16:45:47)

Yes, a Mix Release approach still allows standalone CLI execution. Here's how:

Mix Release vs Escript Comparison

Feature	Escript	Mix Release
Single file binary	Yes	No (directory with files)
Standalone execution	Yes	Yes (via `bin/org_garden` script)
Signal handling (SIGTERM)	Poor	Good (built into BEAM)
Runtime configuration	Limited	Full (`releases.exs`)
Hot code upgrades	No	Optional
Start as daemon	Manual	Built-in (`--daemon`)
Remote shell	No	Yes (`remote`)
Distribution	Single file copy	Tarball or Nix package

How CLI Works with Mix Release

A Mix Release generates a bin/org_garden script that supports multiple commands:

# Run CLI commands (like current escript)
./bin/org_garden eval "OrgGarden.CLI.main(['serve', '/path/to/notes'])"

# Or with a custom entry script
./bin/org_garden serve /path/to/notes

# Also supports daemon mode
./bin/org_garden daemon      # Start as background service
./bin/org_garden remote      # Attach remote shell
./bin/org_garden stop        # Graceful stop with SIGTERM
./bin/org_garden pid         # Get PID

Recommended Approach: Support Both Modes

We can structure the release to support:

CLI mode (one-shot commands like build, export)
Service mode (long-running serve with proper supervision)

# rel/overlays/bin/org-garden (custom entry script)
#!/bin/sh
case "$1" in
  serve)
    # Start as a supervised service
    exec "$RELEASE_ROOT/bin/org_garden" start "$@"
    ;;
  build|export)
    # Run as one-shot command
    exec "$RELEASE_ROOT/bin/org_garden" eval "OrgGarden.CLI.main(System.argv())"
    ;;
  *)
    # Pass through to release commands (daemon, remote, stop, etc.)
    exec "$RELEASE_ROOT/bin/org_garden" "$@"
    ;;
esac

This gives you:

org-garden serve /notes — Starts supervised service (blocks, handles SIGTERM)
org-garden build /notes — One-shot build, exits when done
org-garden export /notes — One-shot export
org-garden daemon — Start as background daemon
org-garden stop — Graceful shutdown
org-garden remote — Attach IEx shell to running instance

Trade-off: Distribution

The main downside vs escript is distribution:

Escript: Single org_garden file (~5MB), copy anywhere with Erlang installed
Release: Directory or tarball (~30MB), but includes ERTS (no Erlang needed on target)

For Nix deployment, this is a non-issue since Nix handles the packaging. The release becomes a single Nix package.

Question: Do you want to:

Replace escript entirely with Mix Release (recommended for service use)
Keep both — escript for simple distribution, release for service deployment
Hybrid — Mix Release with bundled ERTS for fully standalone deployment (no Erlang/Nix needed on target)

User (2026-02-21 16:49:13)

How does elixir projects usually handle services that also offers CLI tools?

Agent (2026-02-21 16:49:15)

Great question. Let me research how established Elixir projects handle this pattern.

Tool Call [completed]: webfetch

Tool: fetch Timestamp: 2026-02-21 16:49:17

mix release — Mix v1.19.5    

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# mix release (Mix v1.19.5)

[View Source](https://github.com/elixir-lang/elixir/blob/v1.19.5/lib/mix/lib/mix/tasks/release.ex#L5 "View Source")

Assembles a self-contained release for the current project:

$ MIX_ENV=prod mix release $ MIX_ENV=prod mix release NAME


Once a release is assembled, it can be packaged and deployed to a target, as long as the target runs on the same operating system (OS) distribution and version as the machine running the [`mix release`](Mix.Tasks.Release.html) command. Windows releases also require Microsoft Visual C++ Runtime.

A release can be configured in your `mix.exs` file under the `:releases` key inside `def project`:

def project do [ releases: [ demo: [ include_executables_for: [:unix], applications: [runtime_tools: :permanent] ],

  ...
]

] end


You can specify multiple releases where the key is the release name and the value is a keyword list with the release configuration. Releasing a certain name is done with:

$ MIX_ENV=prod mix release demo


If the given name does not exist, an error is raised.

If [`mix release`](Mix.Tasks.Release.html) is invoked, without specifying a release name, and there are multiple releases configured, an error will be raised unless you set `default_release: NAME` at the root of your project configuration.

If [`mix release`](Mix.Tasks.Release.html) is invoked and there are no releases configured, a release is assembled using the application name and default values.

## [](#module-why-releases)Why releases?

Releases allow developers to precompile and package all of their code and the runtime into a single unit. The benefits of releases are:

-   Code preloading. The VM has two mechanisms for loading code: interactive and embedded. By default, it runs in the interactive mode which dynamically loads modules when they are used for the first time. The first time your application calls [`Enum.map/2`](https://hexdocs.pm/elixir/Enum.html#map/2), the VM will find the [`Enum`](https://hexdocs.pm/elixir/Enum.html) module and load it. There's a downside: when you start a new server in production, it may need to load many other modules, causing the first requests to have an unusual spike in response time. With releases, the system preloads all modules and guarantees your system is ready to handle requests after booting.
    
-   Configuration and customization. Releases give developers fine grained control over system configuration and the VM flags used to start the system.
    
-   Self-contained. A release does not require the source code to be included in your production artifacts. All of the code is precompiled and packaged. Releases do not even require Erlang or Elixir in your servers, as it includes the Erlang VM and its runtime by default. Furthermore, both Erlang and Elixir standard libraries are stripped to bring only the parts you are actually using.
    
-   Multiple releases. You can assemble different releases with different configuration per application or even with different applications altogether.
    
-   Management scripts. Releases come with scripts to start, restart, connect to the running system remotely, execute RPC calls, run as daemon, run as a Windows service, and more.
    

## [](#module-running-the-release)Running the release

Once a release is assembled, you can start it by calling `bin/RELEASE_NAME start` inside the release. In production, you would do:

$ MIX_ENV=prod mix release $ _build/prod/rel/my_app/bin/my_app start


`bin/my_app start` will start the system connected to the current standard input/output, where logs are also written to by default. This is the preferred way to run the system. Many tools, such as `systemd`, platforms as a service, such as Heroku, and many containers platforms, such as Docker, are capable of processing the standard input/output and redirecting the log contents elsewhere. Those tools and platforms also take care of restarting the system in case it crashes.

You can also execute one-off commands, run the release as a daemon on Unix-like system, or install it as a service on Windows. We will take a look at those next. You can also list all available commands by invoking `bin/RELEASE_NAME`.

### [](#module-one-off-commands-eval-and-rpc)One-off commands (eval and rpc)

If you want to invoke specific modules and functions in your release, you can do so in two ways: using `eval` or `rpc`.

$ bin/RELEASE_NAME eval "IO.puts(:hello)" $ bin/RELEASE_NAME rpc "IO.puts(:hello)"


The `eval` command starts its own instance of the VM but without starting any of the applications in the release and without starting distribution. For example, if you need to do some prep work before running the actual system, like migrating your database, `eval` can be a good fit. Just keep in mind any application you may use during eval has to be explicitly started.

You can start an application by calling [`Application.ensure_all_started/1`](https://hexdocs.pm/elixir/Application.html#ensure_all_started/1). From Elixir v1.16, it is guaranteed the applications have been at least loaded. In earlier versions, if you needed to load applications but not start them, you also needed to call [`Application.load/1`](https://hexdocs.pm/elixir/Application.html#load/1).

Another way to run commands is with `rpc`, which will connect to the system currently running and instruct it to execute the given expression. This means you need to guarantee the system was already started and be careful with the instructions you are executing. You can also use `remote` to connect a remote IEx session to the system.

#### Helper module

As you operate your system, you may find yourself running some piece of code as a one-off command quite often. You may consider creating a module to group these tasks:

lib/my_app/release_tasks.ex

defmodule MyApp.ReleaseTasks do def eval_purge_stale_data() do # Eval commands needs to start the app before # Or Application.load(:my_app) if you can't start it Application.ensure_all_started(:my_app)

# Code that purges stale data
...

end

def rpc_print_connected_users() do # Code that print users connected to the current running system ... end end


In the example above, we prefixed the function names with the command name used to execute them, but that is entirely optional.

And to run them:

$ bin/RELEASE_NAME eval "MyApp.ReleaseTasks.eval_purge_stale_data()" $ bin/RELEASE_NAME rpc "MyApp.ReleaseTasks.rpc_print_connected_users()"


### [](#module-daemon-mode-unix-like)Daemon mode (Unix-like)

You can run the release in daemon mode with the command:

$ bin/RELEASE_NAME daemon


In daemon mode, the system is started on the background via [`run_erl`](https://www.erlang.org/doc/apps/erts/run_erl_cmd.html). You may also want to enable [`:heart`](https://www.erlang.org/doc/apps/kernel/heart.html) in daemon mode so it automatically restarts the system in case of crashes. See the generated `releases/RELEASE_VSN/env.sh` file.

The daemon will write all of its standard output to the `tmp/log/` directory in the release root. You can watch the log file by doing `tail -f tmp/log/erlang.log.1` or similar. Once files get too large, the index suffix will be incremented. A developer can also attach to the standard input of the daemon by invoking `to_erl tmp/pipe/` from the release root. However, note that attaching to the system should be done with extreme care, since the usual commands for exiting an Elixir system, such as hitting Ctrl+C twice or Ctrl+\\, will actually shut down the daemon. Therefore, using `bin/RELEASE_NAME remote` should be preferred, even in daemon mode.

You can customize the tmp directory used both for logging and for piping in daemon mode by setting the `RELEASE_TMP` environment variable. See the "Customization" section.

### [](#module-services-mode-windows)Services mode (Windows)

While daemons are not available on Windows, it is possible to install a released system as a service on Windows with the help of [`erlsrv`](https://www.erlang.org/doc/apps/erts/erlsrv_cmd.html). This can be done by running:

$ bin/RELEASE_NAME install


Once installed, the service must be explicitly managed via the `erlsrv` executable, which is included in the `erts-VSN/bin` directory. The service is not started automatically after installing.

For example, if you have a release named `demo`, you can install the service and then start it from the release root as follows:

$ bin/demo install $ erts-VSN/bin/erlsrv.exe start demo_demo


The name of the service is `demo_demo` because the name is built by concatenating the node name with the release name. Since Elixir automatically uses the same name for both, the service will be referenced as `demo_demo`.

The `install` command must be executed as an administrator.

### [](#module-bin-release_name-commands)`bin/RELEASE_NAME` commands

The following commands are supported by `bin/RELEASE_NAME`:

start Starts the system start_iex Starts the system with IEx attached daemon Starts the system as a daemon (Unix-like only) daemon_iex Starts the system as a daemon with IEx attached (Unix-like only) install Installs this system as a Windows service (Windows only) eval "EXPR" Executes the given expression on a new, non-booted system rpc "EXPR" Executes the given expression remotely on the running system remote Connects to the running system via a remote shell restart Restarts the running system via a remote command stop Stops the running system via a remote command pid Prints the operating system PID of the running system via a remote command version Prints the release name and version to be booted


## [](#module-deployments)Deployments

### [](#module-requirements)Requirements

A release is built on a **host**, a machine which contains Erlang, Elixir, and any other dependencies needed to compile your application. A release is then deployed to a **target**, potentially the same machine as the host, but usually separate, and often there are many targets (either multiple instances, or the release is deployed to heterogeneous environments).

To deploy straight from a host to a separate target, the following must be the same between the host and the target:

-   Target architecture (for example, x86\_64 or ARM)
-   Target vendor + operating system (for example, Windows, Linux, or Darwin/macOS)
-   Target ABI (for example, musl or gnu)

This is often represented in the form of target triples, for example, `x86_64-unknown-linux-gnu`, `x86_64-unknown-linux-musl`, `x86_64-apple-darwin`. If you are building on a MacBook (`x86_64-apple-darwin`) and trying to deploy to a typical Ubuntu machine (`x86_64-unknown-linux-gnu`), the release will not work. Instead you should build the release on a `x86_64-unknown-linux-gnu` host.

Typically, different versions of Erlang VM and Elixir are available for different targets via package managers, precompiled artifacts, and similar. However, to deploy from a host to a separate target, you must also guarantee that any dependency with NIFs (Natively-Implemented Functions) are compiled for the same triplet. As we will see, this can be done in different ways, such as releasing on the target itself, or by using virtual machines or containers, usually as part of your release pipeline.

In addition to matching the target triple, it is also important that the target has all of the system packages that your application will need at runtime. A common one is the need for OpenSSL when building an application that uses `:crypto` or `:ssl`, which is dynamically linked to the Erlang VM. Project dependencies containing NIFs (natively-implemented functions) may also dynamically link to system libraries, so check those accordingly.

Of course, some operating systems and package managers can differ between versions, so if your goal is to have full compatibility between host and target, it is best to ensure the operating system and system package manager have the same versions on host and target. This may even be a requirement in some systems, especially so with package managers that try to create fully reproducible environments (Nix, Guix).

### [](#module-using-matching-host-and-target)Using matching host and target

There are a couple of ways to guarantee that a release is built on a host with the same properties as the target. A simple option is to fetch the source, compile the code and assemble the release on the target itself. It would be something like this:

$ git clone remote://path/to/my_app.git my_app_source $ cd my_app_source $ mix deps.get --only prod $ MIX_ENV=prod mix release $ _build/prod/rel/my_app/bin/my_app start


If you prefer, you can also compile the release to a separate directory, so you can erase all source after the release is assembled:

$ git clone remote://path/to/my_app.git my_app_source $ cd my_app_source $ mix deps.get --only prod $ MIX_ENV=prod mix release --path ../my_app_release $ cd ../my_app_release $ rm -rf ../my_app_source $ bin/my_app start


However, this option can be expensive if you have multiple production nodes or if the release assembling process is a long one, as each node needs to individually assemble the release.

You can automate this process in a couple different ways. One option is to make it part of your Continuous Integration (CI) / Continuous Deployment (CD) pipeline. When you have a CI/CD pipeline, it is common that the machines in your CI/CD pipeline run on the exact same target triple as your production servers (if they don't, they should). In this case, you can assemble the release at the end of your CI/CD pipeline by calling `MIX_ENV=prod mix release` and push the artifact to S3 or any other network storage. To perform the deployment, your production machines can fetch the deployment from the network storage and run `bin/my_app start`.

### [](#module-using-images)Using images

Another mechanism to automate deployments is to use images, such as Amazon Machine Images, or container platforms, such as Docker. For instance, you can use Docker to run locally a system with the exact same target triple as your production servers. Inside the container, you can invoke `MIX_ENV=prod mix release` and build a complete image and/or container with the operating system, all dependencies as well as the releases.

However, when building such images on your machine, those technologies use emulation which may not interplay well with Erlang VM's JIT (just-in time) compiler. To address this, you can set this environment variable on your build stage:

ENV ERL_AFLAGS "+JMsingle true"


## [](#module-shutting-down)Shutting down

Once a system is deployed, shutting down the system can be done by sending SIGINT/SIGTERM to the system, which is what most containers, platforms and tools do, or by explicitly invoking `bin/RELEASE_NAME stop`. Once the system receives the shutdown request, each application and their respective supervision trees will stop, one by one, in the opposite order that they were started.

## [](#module-customization)Customization

There are a couple ways in which developers can customize the generated artifacts inside a release.

### [](#module-options)Options

The following options can be set inside your `mix.exs` on each release definition:

-   `:applications` - a keyword list with application names as keys and their mode as value. By default `:applications` includes the current application and all applications the current application depends on, recursively. You can include new applications or change the mode of existing ones by listing them here.
    
    The order of the applications given will be preserved as much as possible, with only `:kernel`, `:stdlib`, `:sasl`, and `:elixir` listed before the given application list. The supported values are:
    
    -   `:permanent` (default) - the application is started and the node shuts down if the application terminates, regardless of reason
    -   `:transient` - the application is started and the node shuts down if the application terminates abnormally
    -   `:temporary` - the application is started and the node does not shut down if the application terminates
    -   `:load` - the application is only loaded
    -   `:none` - the application is part of the release but it is neither loaded nor started
    
    If you change the mode of an application, the mode will apply to all its child applications. However, if an application has two parents, the mode of the parent with highest priority wins (where `:permanent` has the highest priority, according to the list above).
    
-   `:strip_beams` - controls if BEAM files should have their debug information, documentation chunks, and other non-essential metadata removed. Defaults to `true`. May be set to `false` to disable stripping. Also accepts `[keep: ["Docs", "Dbgi"]]` to keep certain chunks that are usually stripped. You can also set the `:compress` option to true to enable individual compression of BEAM files, although it is typically preferred to compress the whole release instead.
    
-   `:cookie` - a string representing the Erlang Distribution cookie. If this option is not set, a random cookie is written to the `releases/COOKIE` file when the first release is assembled. At runtime, we will first attempt to fetch the cookie from the `RELEASE_COOKIE` environment variable and then we'll read the `releases/COOKIE` file.
    
    If you are setting this option manually, we recommend the cookie option to be a long and randomly generated string, such as: `Base.encode32(:crypto.strong_rand_bytes(40))`. We also recommend restricting the characters in the cookie to only alphanumeric characters and underscore.
    
-   `:validate_compile_env` - by default a release will match all runtime configuration against any configuration that was marked at compile time in your application of its dependencies via the [`Application.compile_env/3`](https://hexdocs.pm/elixir/Application.html#compile_env/3) function. If there is a mismatch between those, it means your system is misconfigured and unable to boot. You can disable this check by setting this option to false.
    
-   `:path` - the path the release should be installed to. Defaults to `"_build/MIX_ENV/rel/RELEASE_NAME"`.
    
-   `:version` - the release version as a string or `{:from_app, app_name}`. Defaults to the current application version. The `{:from_app, app_name}` format can be used to easily reference the application version from another application. This is particularly useful in umbrella applications.
    
-   `:quiet` - a boolean that controls if releases should write steps to the standard output. Defaults to `false`.
    
-   `:include_erts` - a boolean, string, or anonymous function of arity zero. If a boolean, it indicates whether the Erlang Runtime System (ERTS), which includes the Erlang VM, should be included in the release. The default is `true`, which is also the recommended value. If a string, it represents the path to an existing ERTS installation. If an anonymous function of arity zero, it's a function that returns any of the above (boolean or string).
    
    You may also set this option to `false` if you desire to use the ERTS version installed on the target. Note, however, that the ERTS version on the target must have **the exact version** as the ERTS version used when the release is assembled. Setting it to `false` also disables hot code upgrades. Therefore, `:include_erts` should be set to `false` with caution and only if you are assembling the release on the same server that runs it.
    
-   `:include_executables_for` - a list of atoms detailing for which Operating Systems executable files should be generated for. By default, it is set to `[:unix, :windows]`. You can customize those as follows:
    
    ```
    releases: [
      demo: [
        include_executables_for: [:unix] # Or [:windows] or []
      ]
    ]
    ```
    
-   `:rel_templates_path` - the path to find template files that are copied to the release, such as `vm.args.eex`, `remote.vm.args.eex`, `env.sh.eex` (or `env.bat.eex`), and `overlays`. Defaults to `"rel"` in the project root.
    
-   `:overlays` - a list of directories with extra files to be copied as is to the release. The "overlays" directory at `:rel_templates_path` is always included in this list by default (typically at `"rel/overlays"`). See the "Overlays" section for more information.
    
-   `:steps` - a list of steps to execute when assembling the release. See the "Steps" section for more information.
    
-   `:skip_mode_validation_for` - a list of application names (atoms) specifying applications to skip strict validation of "unsafe" modes. An "unsafe" case is when a parent application mode is `:permanent` but one of the applications it depends on is set to `:load`. Use this with care, as a release with invalid modes may no longer boot without additional tweaks. Defaults to `[]`.
    

Note each release definition can be given as an anonymous function. This is useful if some release attributes are expensive to compute:

releases: [ demo: fn -> [version: @version <> "+" <> git_ref()] end ]


Besides the options above, it is possible to customize the generated release with custom files, by tweaking the release steps or by running custom options and commands on boot. We will detail both approaches next.

### [](#module-overlays)Overlays

Often it is necessary to copy extra files to the release root after the release is assembled. This can be easily done by placing such files in the `rel/overlays` directory. Any file in there is copied as is to the release root. For example, if you have placed a `rel/overlays/Dockerfile` file, the "Dockerfile" will be copied as is to the release root.

If you want to specify extra overlay directories, you can do so with the `:overlays` option. If you need to copy files dynamically, see the "Steps" section.

### [](#module-steps)Steps

It is possible to add one or more steps before and after the release is assembled. This can be done with the `:steps` option:

releases: [ demo: [ steps: [&set_configs/1, :assemble, &copy_extra_files/1] ] ]


The `:steps` option must be a list and it must always include the atom `:assemble`, which does most of the release assembling. You can pass anonymous functions before and after the `:assemble` to customize your release assembling pipeline. Those anonymous functions will receive a [`Mix.Release`](Mix.Release.html) struct and must return the same or an updated [`Mix.Release`](Mix.Release.html) struct. It is also possible to build a tarball of the release by passing the `:tar` step anywhere after `:assemble`. If the release `:path` is not configured, the tarball is created in `_build/MIX_ENV/RELEASE_NAME-RELEASE_VSN.tar.gz` Otherwise it is created inside the configured `:path`.

See [`Mix.Release`](Mix.Release.html) for more documentation on the struct and which fields can be modified. Note that the `:steps` field itself can be modified and it is updated every time a step is called. Therefore, if you need to execute a command before and after assembling the release, you only need to declare the first steps in your pipeline and then inject the last step into the release struct. The steps field can also be used to verify if the step was set before or after assembling the release.

### [](#module-vm-args-and-env-sh-env-bat)vm.args and env.sh (env.bat)

Developers may want to customize the VM flags and environment variables given when the release starts. The simplest way to customize those files is by running [`mix release.init`](Mix.Tasks.Release.Init.html). The Mix task will copy custom `rel/vm.args.eex`, `rel/remote.vm.args.eex`, `rel/env.sh.eex`, and `rel/env.bat.eex` files to your project root. You can modify those files and they will be evaluated every time you perform a new release. Those files are regular EEx templates and they have a single assign, called `@release`, with the [`Mix.Release`](Mix.Release.html) struct.

The `vm.args` and `remote.vm.args` files may contain any of the VM flags accepted by the [`erl` command](https://www.erlang.org/doc/man/erl.html).

The `env.sh` and `env.bat` is used to set environment variables. In there, you can set vars such as `RELEASE_NODE`, `RELEASE_COOKIE`, and `RELEASE_TMP` to customize your node name, cookie and tmp directory respectively. Whenever `env.sh` or `env.bat` is invoked, the variables `RELEASE_ROOT`, `RELEASE_NAME`, `RELEASE_VSN`, and `RELEASE_COMMAND` have already been set, so you can rely on them. See the section on environment variables for more information.

Furthermore, while the `vm.args` files are static, you can use `env.sh` and `env.bat` to dynamically set VM options. For example, if you want to make sure the Erlang Distribution listens only on a given port known at runtime, you can set the following:

case $RELEASE_COMMAND in start*|daemon*) ELIXIR_ERL_OPTIONS="-kernel inet_dist_listen_min $BEAM_PORT inet_dist_listen_max $BEAM_PORT" export ELIXIR_ERL_OPTIONS ;; *) ;; esac


Note we only set the port on start/daemon commands. If you also limit the port on other commands, such as `rpc`, then you will be unable to establish a remote connection as the port will already be in use by the node.

On Windows, your `env.bat` would look like this:

IF NOT %RELEASE_COMMAND:start=%==%RELEASE_COMMAND% ( set ELIXIR_ERL_OPTIONS="-kernel inet_dist_listen_min %BEAM_PORT% inet_dist_listen_max %BEAM_PORT%" )


Inside `env.sh` and `env.bat` files you can access command-line arguments given to release commands. For example, given this `env.sh.eex`:

echo $@


or this `env.bat.eex`:

echo %*


starting the release with `bin/myapp start --foo bar baz` will print `start --foo bar baz`.

### [](#module-epmd-less-deployment)`epmd`\-less deployment

When a distributed Erlang/Elixir node starts, it runs a separate daemon called EPMD (Erlang Port Mapper Daemon) and registers the node name within EPMD. It is possible to skip this additional Operating System process by setting the following flags in your vm.args files:

In vm.args.eex

-start_epmd false -erl_epmd_port 6789

In remote.vm.args.eex

-start_epmd false -erl_epmd_port 6789 -dist_listen false


You can pick any port of your choice.

## [](#module-application-configuration)Application configuration

Mix provides two mechanisms for configuring the application environment of your application and your dependencies: build-time and runtime. On this section, we will learn how those mechanisms apply to releases. An introduction to this topic can be found in the "Configuration" section of the [`Mix`](Mix.html) module.

### [](#module-build-time-configuration)Build-time configuration

Whenever you invoke a `mix` command, Mix loads the configuration in `config/config.exs`, if said file exists. We say that this configuration is a build-time configuration as it is evaluated whenever you compile your code or whenever you assemble the release.

In other words, if your configuration does something like:

import Config config :my_app, :secret_key, System.fetch_env!("MY_APP_SECRET_KEY")


The `:secret_key` key under `:my_app` will be computed on the host machine, whenever the release is built. Therefore if the machine assembling the release not have access to all environment variables used to run your code, loading the configuration will fail as the environment variable is missing. Luckily, Mix also provides runtime configuration, which should be preferred and we will see next.

### [](#module-runtime-configuration)Runtime configuration

To enable runtime configuration in your release, create a file named `config/runtime.exs`:

import Config config :my_app, :secret_key, System.fetch_env!("MY_APP_SECRET_KEY")


This file will be executed whenever your Mix project or your release starts.

Your `config/runtime.exs` file needs to follow three important rules:

-   It MUST `import Config` at the top instead of the deprecated `use Mix.Config`
-   It MUST NOT import any other configuration file via `import_config`
-   It MUST NOT access [`Mix`](Mix.html) in any way, as [`Mix`](Mix.html) is a build tool and it is not available inside releases

If a `config/runtime.exs` exists, it will be copied to your release and executed early in the boot process, when only Elixir and Erlang's main applications have been started.

You can change the path to the runtime configuration file by setting `:runtime_config_path` inside each release configuration. This path is resolved at build time as the given configuration file is always copied to inside the release:

releases: [ demo: [ runtime_config_path: ... ] ]


By setting `:runtime_config_path` to `false` it can be used to prevent a runtime configuration file to be included in the release.

### [](#module-config-providers)Config providers

Releases also supports custom mechanisms, called config providers, to load any sort of runtime configuration to the system while it boots. For instance, if you need to access a vault or load configuration from a JSON file, it can be achieved with config providers. The runtime configuration outlined in the previous section is handled by the [`Config.Reader`](https://hexdocs.pm/elixir/Config.Reader.html) provider. See the [`Config.Provider`](https://hexdocs.pm/elixir/Config.Provider.html) module for more information and more examples.

The following options can be set inside your releases key in your `mix.exs` to control how config providers work:

-   `:reboot_system_after_config` - reboot the system after configuration so you can configure system applications, such as `:kernel` and `:stdlib`, in your `config/runtime.exs`. Generally speaking, it is best to configure `:kernel` and `:stdlib` using the `vm.args` file but this option is available for those who need more complex configuration. When set to `true`, the release will first boot in interactive mode to compute a config file and write it to the "tmp" directory. Then it reboots in the configured `RELEASE_MODE`. You can configure the "tmp" directory by setting the `RELEASE_TMP` environment variable, either explicitly or inside your `releases/RELEASE_VSN/env.sh` (or `env.bat` on Windows). Defaults to `true` if using the deprecated `config/releases.exs`, `false` otherwise. Be careful of which libraries you load when setting this option to true, if a library is loaded early during configuration and it includes native code, it may not actually be able to restart cleanly.
    
-   `:prune_runtime_sys_config_after_boot` - if `:reboot_system_after_config` is set, every time your system boots, the release will write a config file to your tmp directory. These configuration files are generally small. But if you are concerned with disk space or if you have other restrictions, you can ask the system to remove said config files after boot. The downside is that you will no longer be able to restart the system internally (neither via [`System.restart/0`](https://hexdocs.pm/elixir/System.html#restart/0) nor `bin/RELEASE_NAME restart`). If you need a restart, you will have to terminate the Operating System process and start a new one. Defaults to `false`.
    
-   `:start_distribution_during_config` - if `:reboot_system_after_config` is set, releases only start the Erlang VM distribution features after the config files are evaluated. You can set it to `true` if you need distribution during configuration. Defaults to `false`.
    
-   `:config_providers` - a list of tuples with custom config providers. See [`Config.Provider`](https://hexdocs.pm/elixir/Config.Provider.html) for more information. Defaults to `[]`.
    

### [](#module-customization-and-configuration-summary)Customization and configuration summary

Generally speaking, the following files are available for customizing and configuring the running system:

-   `config/config.exs` (and `config/prod.exs`) - provides build-time application configuration, which are executed when the release is assembled
    
-   `config/runtime.exs` - provides runtime application configuration. It is executed every time your Mix project or your release boots and is further extensible via config providers. If you want to detect you are inside a release, you can check for release specific environment variables, such as `RELEASE_NODE` or `RELEASE_MODE`
    
-   `rel/vm.args.eex` and `rel/remote.vm.args.eex` - template files that are copied into every release and provides static configuration of the Erlang Virtual Machine and other runtime flags. `vm.args` runs on `start`, `daemon`, and `eval` commands. `remote.vm.args` configures the VM for `remote` and `rpc` commands
    
-   `rel/env.sh.eex` and `rel/env.bat.eex` - template files that are copied into every release and are executed on every command to set up environment variables, including specific ones to the VM, and the general environment
    

## [](#module-directory-structure)Directory structure

A release is organized as follows:

bin/ RELEASE_NAME erts-ERTS_VSN/ lib/ APP_NAME-APP_VSN/ ebin/ include/ priv/ releases/ RELEASE_VSN/ consolidated/ elixir elixir.bat env.bat env.sh iex iex.bat remote.vm.args runtime.exs start.boot start.script start_clean.boot start_clean.script sys.config vm.args COOKIE start_erl.data tmp/


We document this structure for completeness. In practice, developers should not modify any of those files after the release is assembled. Instead use env scripts, custom config provider, overlays, and all other mechanisms described here to configure how your release works.

## [](#module-environment-variables)Environment variables

The system sets different environment variables. The following variables are set early on and can only be read by `env.sh` and `env.bat`:

-   `RELEASE_ROOT` - points to the root of the release. If the system includes ERTS, then it is the same as [`:code.root_dir/0`](https://www.erlang.org/doc/apps/kernel/code.html#root_dir/0). This variable is always computed and it cannot be set to a custom value
    
-   `RELEASE_COMMAND` - the command given to the release, such as `"start"`, `"remote"`, `"eval"`, and so on. This is typically accessed inside `env.sh` and `env.bat` to set different environment variables under different conditions. Note, however, that `RELEASE_COMMAND` has not been validated by the time `env.sh` and `env.bat` are called, so it may be empty or contain invalid values. This variable is always computed and it cannot be set to a custom value
    
-   `RELEASE_NAME` - the name of the release. It can be set to a custom value when invoking the release
    
-   `RELEASE_VSN` - the version of the release, otherwise the latest version is used. It can be set to a custom value when invoking the release. The custom value must be an existing release version in the `releases/` directory
    
-   `RELEASE_PROG` - the command line executable used to start the release
    

The following variables can be set before you invoke the release or inside `env.sh` and `env.bat`:

-   `RELEASE_COOKIE` - the release cookie. By default uses the value in `releases/COOKIE`. It can be set to a custom value
    
-   `RELEASE_NODE` - the release node name, in the format `name` or optionally `name@host` if running in distributed mode. It can be set to a custom value. The name part must be made only of letters, digits, underscores, and hyphens
    
-   `RELEASE_SYS_CONFIG` - the location of the sys.config file. It can be set to a custom path and it must not include the `.config` extension
    
-   `RELEASE_VM_ARGS` - the location of the vm.args file. It can be set to a custom path
    
-   `RELEASE_REMOTE_VM_ARGS` - the location of the remote.vm.args file. It can be set to a custom path
    
-   `RELEASE_TMP` - the directory in the release to write temporary files to. It can be set to a custom directory. It defaults to `$RELEASE_ROOT/tmp`
    
-   `RELEASE_MODE` - if the release should load code on demand (interactive) or preload it (embedded). Defaults to "embedded", which increases boot time but it means the runtime will respond faster as it doesn't have to load code. Choose interactive if you need to decrease boot time and reduce memory usage on boot. It applies only to start/daemon/install commands
    
-   `RELEASE_DISTRIBUTION` - how do we want to run the distribution. May be `name` (long names), `sname` (short names) or `none` (distribution is not started automatically). Defaults to `sname`. When connecting nodes across hosts, you typically want to set this to `name` (required to use IPs as host names)
    
-   `RELEASE_BOOT_SCRIPT` - the name of the boot script to use when starting the release. This script is used when running commands such as `start` and `daemon`. The boot script is expected to be located at the path `releases/RELEASE_VSN/RELEASE_BOOT_SCRIPT.boot`. Defaults to `start`
    
-   `RELEASE_BOOT_SCRIPT_CLEAN` - the name of the boot script used when starting the release clean, without your application or its dependencies. This script is used by commands such as `eval`, `rpc`, and `remote`. The boot script is expected to be located at the path `releases/RELEASE_VSN/RELEASE_BOOT_SCRIPT_CLEAN.boot`. Defaults to `start_clean`
    

## [](#module-umbrellas)Umbrellas

Releases are well integrated with umbrella projects, allowing you to release one or more subsets of your umbrella children. The only difference between performing a release in the umbrella project compared to a regular application is that umbrellas require you to explicitly list your release and the starting point for each release. For example, imagine this umbrella applications:

my_app_umbrella/ apps/ my_app_core/ my_app_event_processing/ my_app_web/


where both `my_app_event_processing` and `my_app_web` depend on `my_app_core` but they do not depend on each other.

Inside your umbrella, you can define multiple releases:

releases: [ web_and_event_processing: [ applications: [ my_app_event_processing: :permanent, my_app_web: :permanent ] ],

web_only: [ applications: [my_app_web: :permanent] ],

event_processing_only: [ applications: [my_app_event_processing: :permanent] ] ]


Note you don't need to define all applications in `:applications`, only the entry points. Also remember that the recommended mode for all applications in the system is `:permanent`.

Finally, keep in mind it is not required for you to assemble the release from the umbrella root. You can also assemble the release from each child application individually. Doing it from the root, however, allows you to include two applications that do not depend on each other as part of the same release.

## [](#module-hot-code-upgrades)Hot Code Upgrades

Erlang and Elixir are sometimes known for the capability of upgrading a node that is running in production without shutting down that node. However, this feature is not supported out of the box by Elixir releases.

The reason we don't provide hot code upgrades is because they are very complicated to perform in practice, as they require careful coding of your processes and applications as well as extensive testing. Given most teams can use other techniques that are language agnostic to upgrade their systems, such as Blue/Green deployments, Canary deployments, Rolling deployments, and others, hot upgrades are rarely a viable option. Let's understand why.

In a hot code upgrade, you want to update a node from version A to version B. To do so, the first step is to write recipes for every application that changed between those two releases, telling exactly how the application changed between versions, those recipes are called `.appup` files. While some of the steps in building `.appup` files can be automated, not all of them can. Furthermore, each process in the application needs to be explicitly coded with hot code upgrades in mind. Let's see an example. Imagine your application has a counter process as a GenServer:

defmodule Counter do use GenServer

def start_link(_) do GenServer.start_link(MODULE, :ok, name: MODULE) end

def bump do GenServer.call(MODULE, :bump) end

Callbacks

def init(:ok) do {:ok, 0} end

def handle_call(:bump, counter) do {:reply, :ok, counter + 1} end end


You add this process as part of your supervision tree and ship version 0.1.0 of your system. Now let's imagine that on version 0.2.0 you added two changes: instead of `bump/0`, that always increments the counter by one, you introduce `bump/1` that passes the exact value to bump the counter. You also change the state, because you want to store the maximum bump value:

defmodule Counter do use GenServer

def start_link(_) do GenServer.start_link(MODULE, :ok, name: MODULE) end

def bump(by) do GenServer.call(MODULE, {:bump, by}) end

Callbacks

def init(:ok) do {:ok, {0, 0}} end

def handle_call({:bump, by}, {counter, max}) do {:reply, :ok, {counter + by, max(max, by)}} end end


If you were to perform a hot code upgrade in such an application, it would crash, because in the initial version the state was just a counter but in the new version the state is a tuple. Furthermore, you changed the format of the `call` message from `:bump` to `{:bump, by}` and the process may have both old and new messages temporarily mixed, so we need to handle both. The final version would be:

defmodule Counter do use GenServer

def start_link(_) do GenServer.start_link(MODULE, :ok, name: MODULE) end

def bump(by) do GenServer.call(MODULE, {:bump, by}) end

Callbacks

def init(:ok) do {:ok, {0, 0}} end

def handle_call(:bump, {counter, max}) do {:reply, :ok, {counter + 1, max(max, 1)}} end

def handle_call({:bump, by}, {counter, max}) do {:reply, :ok, {counter + by, max(max, by)}} end

def code_change(_, counter, _) do {:ok, {counter, 0}} end end


Now you can proceed to list this process in the `.appup` file and hot code upgrade it. This is one of the many steps necessary to perform hot code upgrades and it must be taken into account by every process and application being upgraded in the system. The [`.appup` cookbook](https://www.erlang.org/doc/design_principles/appup_cookbook.html) provides a good reference and more examples.

Once `.appup`s are created, the next step is to create a `.relup` file with all instructions necessary to update the release itself. Erlang documentation does provide a chapter on [Creating and upgrading a target system](https://www.erlang.org/doc/system_principles/create_target.html). [Learn You Some Erlang has a chapter on hot code upgrades](https://learnyousomeerlang.com/relups).

Overall, there are many steps, complexities and assumptions made during hot code upgrades, which is ultimately why they are not provided by Elixir out of the box. However, hot code upgrades can still be achieved by teams who desire to implement those steps on top of [`mix release`](Mix.Tasks.Release.html) in their projects or as separate libraries.

## [](#module-command-line-options)Command line options

-   `--force` - forces recompilation
-   `--no-archives-check` - does not check archive
-   `--no-deps-check` - does not check dependencies
-   `--no-elixir-version-check` - does not check Elixir version
-   `--no-compile` - does not compile before assembling the release
-   `--overwrite` - overwrite existing files instead of prompting the user for action
-   `--path` - the path of the release
-   `--quiet` - does not write progress to the standard output
-   `--version` - the version of the release

Go to package docs [Download ePub version](Mix.epub "ePub version")

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Tool Call [completed]: task

Tool: other Timestamp: 2026-02-21 16:50:38

task_id: ses_37f1bd674ffeO53rrE00gDEhCE (for resuming to continue this task if needed)

<task_result>
I now have enough information to provide a comprehensive summary. Let me compile the findings:

---

# Elixir CLI + Service Patterns: Research Summary

## Overview

After researching Livebook, Phoenix, Mix, ExUnit, Oban, Burrito, and Bakeware, here are the common patterns used in the Elixir ecosystem for applications that need to function as both CLI tools and long-running services.

---

## 1. CLI Entry Point Patterns

### Pattern A: Escript with Main Module (Livebook)

Livebook uses **escript** with a custom `main/1` function that dispatches to subcommands:

```elixir
# lib/livebook_cli.ex
defmodule LivebookCLI do
  def main(args) do
    {:ok, _} = Application.ensure_all_started(:elixir)
    :ok = Application.load(:livebook)
    
    case args do
      ["server" | args] -> LivebookCLI.Server.call(args)
      ["deploy" | args] -> LivebookCLI.Deploy.call(args)
      [arg] when arg in ["--help", "-h"] -> display_help()
      [arg] when arg in ["--version", "-v"] -> display_version()
      _ -> display_usage()
    end
  end
end

Key features:

Task behaviour pattern with call/1 and usage/0 callbacks
Extracts priv directory from escript archive at runtime
Starts the full OTP application with Process.sleep(:infinity) for server mode

# mix.exs escript configuration
defp escript do
  [
    main_module: LivebookCLI,
    app: nil,
    emu_args: "-epmd_module Elixir.Livebook.EPMD"
  ]
end

Pattern B: Mix Tasks (Phoenix)

Phoenix uses Mix tasks for CLI operations that run within a project:

# lib/mix/tasks/phx.server.ex
defmodule Mix.Tasks.Phx.Server do
  use Mix.Task

  @impl true
  def run(args) do
    Application.put_env(:phoenix, :serve_endpoints, true, persistent: true)
    Mix.Tasks.Run.run(run_args() ++ args)
  end

  defp run_args do
    if iex_running?(), do: [], else: ["--no-halt"]
  end
end

Key features:

Uses use Mix.Task for automatic task registration
Leverages @shortdoc and @moduledoc for help
@requirements attribute for dependencies (e.g., ["app.config"])
Wraps Mix.Tasks.Run with appropriate flags

Pattern C: Mix CLI Module (Mix itself)

Mix has a dedicated CLI module that parses arguments and dispatches:

# lib/mix/lib/mix/cli.ex
defmodule Mix.CLI do
  def main(args \\ System.argv()) do
    Mix.start()
    
    case check_for_shortcuts(args) do
      :help -> display_help()
      :version -> display_version()
      nil -> proceed(args)
    end
  end

  defp proceed(args) do
    load_mix_exs(args)
    {task, args} = get_task(args)
    run_task(task, args)
  end
end

2. Distribution Methods

Method 1: Escript (Livebook primary method)

Pros:

Single file distribution
No external dependencies beyond Erlang/Elixir installation
Fast startup for CLI tools

Cons:

Requires Erlang/Elixir installed on target machine
Cannot include native dependencies easily

# mix.exs
def project do
  [
    escript: [
      main_module: MyApp.CLI,
      app: nil,  # Don't start app automatically
      include_priv_for: [:my_app]
    ]
  ]
end

Method 2: Mix Releases (Phoenix, Livebook production)

Pros:

Bundles ERTS (Erlang runtime)
Supports hot upgrades
Multiple boot scripts
Configuration providers

Cons:

Larger file size
Platform-specific builds

# mix.exs
defp releases do
  [
    my_app: [
      applications: [my_app: :permanent],
      include_executables_for: [:unix, :windows],
      steps: [:assemble, &custom_step/1]
    ]
  ]
end

Release scripts support multiple commands:

bin/my_app start - Start as daemon
bin/my_app start_iex - Start with IEx
bin/my_app eval "expr" - Evaluate expression
bin/my_app rpc "expr" - Remote call to running node
bin/my_app remote - Connect to running node

Method 3: Burrito (Standalone binaries)

For completely standalone distribution without any runtime requirements:

# mix.exs
def releases do
  [
    my_cli: [
      steps: [:assemble, &Burrito.wrap/1],
      burrito: [
        targets: [
          macos: [os: :darwin, cpu: :x86_64],
          linux: [os: :linux, cpu: :x86_64],
          windows: [os: :windows, cpu: :x86_64]
        ]
      ]
    ]
  ]
end

Key features:

Cross-compilation from Linux/macOS
Self-extracting archives with Zig wrapper
Embeds ERTS for each platform
Access args via Burrito.Util.Args.argv()
Maintenance commands: --bw-info, --bw-install

Method 4: Bakeware (Deprecated, use Burrito)

Similar to Burrito but older. Uses Bakeware.Script behaviour:

defmodule MyApp.Main do
  use Bakeware.Script

  @impl Bakeware.Script
  def main(args) do
    IO.puts("Hello!")
    0  # Exit code
  end
end

3. Service vs CLI Distinction Patterns

Pattern 1: Command Dispatch (Livebook)

defmodule LivebookCLI.Server do
  @behaviour LivebookCLI.Task

  def call(args) do
    config_entries = parse_and_configure(args)
    
    case Application.ensure_all_started(:livebook) do
      {:ok, _} ->
        open_browser_if_requested(args)
        Process.sleep(:infinity)  # Keep running as service
      {:error, error} ->
        raise "Failed to start"
    end
  end
end

Pattern 2: Environment Configuration (Phoenix)

# config/runtime.exs
if System.get_env("PHX_SERVER") do
  config :my_app, MyAppWeb.Endpoint, server: true
end

Combined with:

# Application.start
def start(_type, _args) do
  children = [
    MyAppWeb.Endpoint  # Only starts server if configured
  ]
  Supervisor.start_link(children, strategy: :one_for_one)
end

Pattern 3: Application Module Callback

def application do
  [
    mod: {MyApp.Application, []},
    extra_applications: [:logger]
  ]
end

# For CLI tools that exit
defmodule MyApp.Application do
  def start(_type, _args) do
    result = MyApp.CLI.run(System.argv())
    System.halt(result)  # Exit with code
  end
end

# For services that keep running
defmodule MyApp.Application do
  def start(_type, _args) do
    children = [MyApp.Server]
    Supervisor.start_link(children, strategy: :one_for_one)
  end
end

Pattern 4: Conditional Supervision Trees (Oban)

Oban runs as part of your application's supervision tree:

# lib/my_app/application.ex
def start(_type, _args) do
  children = [
    MyApp.Repo,
    {Oban, Application.fetch_env!(:my_app, Oban)}
  ]
  Supervisor.start_link(children, strategy: :one_for_one)
end

CLI operations use Mix tasks that connect to the running application.

4. Recommended Architecture for CLI + Service

Based on the research, here's the recommended pattern:

lib/
├── my_app/
│   ├── application.ex      # OTP Application
│   └── ...                  # Business logic
├── my_app_cli.ex            # CLI entry point (for escript)
├── my_app_cli/
│   ├── task.ex              # Task behaviour
│   ├── server.ex            # "server" subcommand
│   ├── eval.ex              # "eval" subcommand  
│   └── utils.ex             # CLI utilities
└── mix/
    └── tasks/
        └── my_app/
            └── server.ex    # Mix task alternative

CLI Entry Point

defmodule MyAppCLI do
  def main(args) do
    {:ok, _} = Application.ensure_all_started(:elixir)
    :ok = Application.load(:my_app)

    case args do
      ["server" | rest] -> MyAppCLI.Server.call(rest)
      ["eval", expr | _] -> MyAppCLI.Eval.call(expr)
      ["version" | _] -> IO.puts(MyApp.version())
      ["--help" | _] -> IO.puts(usage())
      ["-h" | _] -> IO.puts(usage())
      _ -> IO.puts(usage())
    end
  end

  def usage do
    """
    Usage: my_app <command> [options]

    Commands:
      server    Start the application server
      eval      Evaluate an expression
      version   Print version

    Use "my_app <command> --help" for command-specific help.
    """
  end
end

Task Behaviour

defmodule MyAppCLI.Task do
  @callback usage() :: String.t()
  @callback call(args :: [String.t()]) :: :ok | {:error, term()}
end

Server Command

defmodule MyAppCLI.Server do
  @behaviour MyAppCLI.Task

  def usage, do: "Usage: my_app server [--port PORT] [--host HOST]"

  def call(args) do
    {opts, _, _} = OptionParser.parse(args, 
      strict: [port: :integer, host: :string, help: :boolean]
    )

    if opts[:help] do
      IO.puts(usage())
    else
      configure(opts)
      {:ok, _} = Application.ensure_all_started(:my_app)
      Process.sleep(:infinity)
    end
  end

  defp configure(opts) do
    if port = opts[:port] do
      Application.put_env(:my_app, :port, port, persistent: true)
    end
  end
end

5. Summary of Patterns

Project	Primary Method	CLI Pattern	Service Pattern
Livebook	Escript + Release	Custom main/1 with subcommands	`Process.sleep(:infinity)` after app start
Phoenix	Mix Release	Mix Tasks (`use Mix.Task`)	`server: true` endpoint config
Mix	Bundled with Elixir	CLI module with task dispatch	N/A (build tool)
ExUnit	Library	`ExUnit.start()` with `System.at_exit`	N/A (test runner)
Oban	Library	Mix Tasks + Web UI	Supervision tree child
Burrito	Standalone binary	`Burrito.Util.Args.argv()`	Full OTP application

Key Takeaways

Use Mix Tasks for operations that run within a Mix project context
Use Escript for standalone CLI tools when Erlang is available
Use Mix Releases for production deployments of services
Use Burrito for zero-dependency standalone binaries
Separate concerns: CLI parsing in one module, business logic in another
Use Process.sleep(:infinity) to keep a CLI-started service running
Use Application config to toggle server/CLI behavior
Define a Task behaviour for consistent subcommand interface </task_result>

## Agent (2026-02-21 16:50:40)

Based on my research, here's how Elixir projects typically handle the CLI + service pattern:

## Common Patterns in the Ecosystem

### 1. **Livebook Pattern** (Most relevant to org-garden)

Livebook uses an **escript for CLI** but starts the full OTP application for service mode:

```elixir
defmodule LivebookCLI do
  def main(args) do
    :ok = Application.load(:livebook)
    
    case args do
      ["server" | rest] -> LivebookCLI.Server.call(rest)  # Long-running
      ["deploy" | rest] -> LivebookCLI.Deploy.call(rest)  # One-shot
      _ -> display_usage()
    end
  end
end

defmodule LivebookCLI.Server do
  def call(args) do
    configure(args)
    {:ok, _} = Application.ensure_all_started(:livebook)
    Process.sleep(:infinity)  # Keep running
  end
end

2. Mix Release with `eval` (Production deployments)

A Mix Release provides both modes out of the box:

# One-shot commands (CLI)
bin/my_app eval "MyApp.CLI.build('/path')"

# Long-running service
bin/my_app start
bin/my_app daemon

3. Custom Release Script (Best of both worlds)

Projects often add a wrapper script in rel/overlays/bin/:

#!/bin/sh
# rel/overlays/bin/my-app-cli
case "$1" in
  serve|daemon)
    exec "$RELEASE_ROOT/bin/my_app" "$@"
    ;;
  build|export)
    exec "$RELEASE_ROOT/bin/my_app" eval "MyApp.CLI.main(System.argv())"
    ;;
  *)
    exec "$RELEASE_ROOT/bin/my_app" "$@"
    ;;
esac

Recommended Approach for org-garden

Based on the research, I recommend Mix Release with a custom CLI module:

                    ┌─────────────────┐
                    │   org-garden    │
                    │  (shell script) │
                    └────────┬────────┘
                             │
              ┌──────────────┼──────────────┐
              ▼              ▼              ▼
        ┌─────────┐    ┌─────────┐    ┌─────────┐
        │  serve  │    │  build  │    │ export  │
        │ (start) │    │ (eval)  │    │ (eval)  │
        └────┬────┘    └────┬────┘    └────┬────┘
             │              │              │
             ▼              ▼              ▼
    Full OTP App      One-shot        One-shot
    with Supervisor   exits when      exits when
    (blocks)          done            done

Implementation Structure

lib/
├── org_garden/
│   ├── application.ex      # OTP Application (service mode)
│   ├── server.ex           # New: encapsulates serve mode startup
│   └── ...
├── org_garden_cli.ex       # CLI dispatcher (kept for escript compat)
└── org_garden_cli/
    ├── commands.ex         # Command implementations
    └── parser.ex           # Argument parsing

Key Files

1. lib/org_garden/application.ex — Conditional startup:

def start(_type, _args) do
  children = [
    {Finch, name: OrgGarden.Finch},
    {Registry, keys: :unique, name: OrgGarden.Registry},
    {DynamicSupervisor, name: OrgGarden.DynamicSupervisor}
  ]
  
  # Service components started dynamically via OrgGarden.Server.start/1
  Supervisor.start_link(children, strategy: :one_for_one)
end

2. lib/org_garden/server.ex — Encapsulates service mode:

defmodule OrgGarden.Server do
  def start(opts) do
    # Initial export
    run_initial_pipeline(opts)
    
    # Start supervised watcher + quartz
    DynamicSupervisor.start_child(
      OrgGarden.DynamicSupervisor,
      {OrgGarden.Supervisor, opts}
    )
  end
  
  def stop do
    # Graceful shutdown
  end
end

3. rel/overlays/bin/org-garden — Unified entry point:

#!/bin/sh
SELF=$(readlink -f "$0")
RELEASE_ROOT=$(dirname "$(dirname "$SELF")")

case "$1" in
  serve)
    shift
    exec "$RELEASE_ROOT/bin/org_garden" start -- serve "$@"
    ;;
  build|export)
    exec "$RELEASE_ROOT/bin/org_garden" eval "OrgGarden.CLI.main(System.argv())" -- "$@"
    ;;
  daemon|stop|remote|pid)
    exec "$RELEASE_ROOT/bin/org_garden" "$@"
    ;;
  *)
    echo "Usage: org-garden <serve|build|export|daemon|stop|remote> [options]"
    ;;
esac

Trade-offs Summary

Approach	Distribution	Signal Handling	Runtime Config	Complexity
Escript only	Single file	Poor	Limited	Low
Release only	Directory/tarball	Good	Full	Medium
Both	Two artifacts	Mixed	Full	Higher
Release + overlay script	Single package	Good	Full	Medium

Questions for You

Do you want to keep escript compatibility for simple mix escript.build distribution, or is Nix packaging sufficient?
For the NixOS service, should serve mode be the only supported mode (with build/export as one-shot systemd ExecStartPre or separate units)?
Should we use Burrito for fully standalone binaries (no Nix/Erlang needed on target), or is

Nix the primary distribution method?## User (2026-02-21 20:05:16)

The release only + overlay script is fine. If not complex, let's keep esript.build. Nix the primary distribution method. The NixOS service should only support serve, as it is a long-running service. If one-shot needed, the package is for that.

Agent (2026-02-21 20:05:19)

Understood. Let me finalize the implementation plan based on your decisions:

Release + overlay script as primary approach
Keep escript for simple builds (if not complex)
Nix as primary distribution
NixOS service only supports serve mode

Final Implementation Plan: org-garden Service Improvements

Summary of Changes

Phase	Description	Files Changed/Added
1	Supervision Tree Integration	`application.ex`, `server.ex` (new), `cli.ex`
2	Configuration System	`config/config.exs`, `config/runtime.exs`, `config.ex` (new)
3	Graceful Shutdown	`quartz.ex`, `watcher.ex`, `server.ex`
4	Health Checks	`health.ex` (new), `mix.exs`
5	Observability	`telemetry.ex` (new), updates to `watcher.ex`, `export.ex`
6	Mix Release	`mix.exs`, `rel/` directory
7	NixOS Module	`nix/module.nix`, `flake.nix`

Phase 1: Supervision Tree Integration

1.1 Refactor `application.ex`

Current state:

children = [
  {Finch, name: OrgGarden.Finch}
]

New state:

children = [
  {Finch, name: OrgGarden.Finch},
  {Registry, keys: :unique, name: OrgGarden.Registry},
  {DynamicSupervisor, name: OrgGarden.DynamicSupervisor, strategy: :one_for_one}
]

1.2 Create `lib/org_garden/server.ex`

New module that encapsulates the "serve" mode lifecycle:

defmodule OrgGarden.Server do
  @moduledoc """
  Manages the serve mode lifecycle.
  
  Handles initial export, starts the supervision tree,
  and provides graceful shutdown.
  """
  use GenServer
  
  def start_link(opts)
  def stop(timeout \\ 5000)
  
  # Callbacks handle:
  # - Initial pipeline run
  # - Starting OrgGarden.Supervisor under DynamicSupervisor
  # - Trapping exits for graceful shutdown
end

1.3 Update `cli.ex`

Changes:

Replace Process.sleep(:infinity) with OrgGarden.Server.start_link(opts) + receive do block
handle_serve/1 starts OrgGarden.Server which blocks properly
Export --watch mode starts Watcher under DynamicSupervisor

Phase 2: Configuration System

2.1 Create `config/config.exs`

import Config

config :org_garden,
  # Defaults (overridden by runtime.exs)
  zotero_url: "http://localhost:23119",
  citation_mode: :warn,
  health_port: 9090

config :logger, :console,
  format: "$time $metadata[$level] $message\n",
  metadata: [:module, :file]

2.2 Create `config/runtime.exs`

import Config

if config_env() == :prod do
  config :org_garden,
    quartz_path: System.fetch_env!("QUARTZ_PATH"),
    node_path: System.get_env("NODE_PATH", "node"),
    notes_dir: System.get_env("NOTES_DIR"),
    output_dir: System.get_env("OUTPUT_DIR"),
    zotero_url: System.get_env("ZOTERO_URL", "http://localhost:23119"),
    bibtex_file: System.get_env("BIBTEX_FILE"),
    citation_mode: parse_citation_mode(System.get_env("CITATION_MODE", "warn")),
    http_port: parse_int(System.get_env("PORT"), 8080),
    ws_port: parse_int(System.get_env("WS_PORT"), 3001),
    health_port: parse_int(System.get_env("HEALTH_PORT"), 9090)
end

2.3 Create `lib/org_garden/config.ex`

defmodule OrgGarden.Config do
  @moduledoc "Centralized configuration access with validation."
  
  def get(key, default \\ nil)
  def get!(key)  # Raises if missing
  def validate!()  # Called at startup, fails fast
end

2.4 Update modules to use `OrgGarden.Config`

Replace System.get_env/1 calls in:

cli.ex — use Config for defaults, CLI args override
quartz.ex — Config.get!(:quartz_path)
transforms/citations.ex — Config.get(:zotero_url)

Phase 3: Graceful Shutdown

3.1 Update `server.ex`

def init(opts) do
  Process.flag(:trap_exit, true)
  # ... start children
end

def terminate(reason, state) do
  Logger.info("Shutting down org-garden server...")
  
  # 1. Stop accepting new file events
  # 2. Wait for in-flight processing (with timeout)
  # 3. Stop Quartz gracefully
  
  :ok
end

3.2 Update `quartz.ex`

Current:

def terminate(_reason, %{port: port}) do
  Port.close(port)
end

New:

def terminate(_reason, %{port: port, os_pid: os_pid}) do
  # Send SIGTERM to Node.js process
  System.cmd("kill", ["-TERM", to_string(os_pid)], stderr_to_stdout: true)
  
  # Wait up to 5 seconds for graceful exit
  receive do
    {^port, {:exit_status, _}} -> :ok
  after
    5000 ->
      System.cmd("kill", ["-KILL", to_string(os_pid)], stderr_to_stdout: true)
  end
  
  :ok
end

Need to capture OS PID in init/1:

{:os_pid, os_pid} = Port.info(port, :os_pid)

3.3 Update `watcher.ex`

Add drain period for pending debounce timers:

def terminate(_reason, state) do
  # Flush pending timers
  Enum.each(state.pending, fn {path, ref} ->
    Process.cancel_timer(ref)
    # Optionally process immediately or log
  end)
  
  OrgGarden.teardown_transforms(state.initialized_transforms)
  :ok
end

Phase 4: Health Checks

4.1 Add dependencies to `mix.exs`

defp deps do
  [
    # Existing
    {:finch, "~> 0.19"},
    {:req, "~> 0.5"},
    {:jason, "~> 1.4"},
    {:file_system, "~> 1.0"},
    
    # New: minimal HTTP server for health checks
    {:bandit, "~> 1.0"},
    {:plug, "~> 1.15"}
  ]
end

4.2 Create `lib/org_garden/health.ex`

defmodule OrgGarden.Health do
  use Plug.Router
  
  plug :match
  plug :dispatch
  
  get "/health/live" do
    send_resp(conn, 200, "ok")
  end
  
  get "/health/ready" do
    checks = %{
      watcher: check_watcher(),
      quartz: check_quartz()
    }
    
    if Enum.all?(checks, fn {_, v} -> v end) do
      send_resp(conn, 200, Jason.encode!(%{status: "ready", checks: checks}))
    else
      send_resp(conn, 503, Jason.encode!(%{status: "not_ready", checks: checks}))
    end
  end
  
  defp check_watcher, do: Process.whereis(OrgGarden.Watcher) != nil
  defp check_quartz, do: Process.whereis(OrgGarden.Quartz) != nil
end

4.3 Add to supervision tree

In application.ex, start Bandit when configured:

children = [
  # ... existing
  {Bandit, plug: OrgGarden.Health, port: Config.get(:health_port, 9090)}
]

Phase 5: Observability

5.1 Create `lib/org_garden/telemetry.ex`

defmodule OrgGarden.Telemetry do
  @moduledoc "Telemetry event definitions and helpers."
  
  def export_start(metadata), do: 
    :telemetry.execute([:org_garden, :export, :start], %{}, metadata)
  
  def export_stop(metadata, measurements), do:
    :telemetry.execute([:org_garden, :export, :stop], measurements, metadata)
  
  # Events:
  # [:org_garden, :export, :start | :stop | :exception]
  # [:org_garden, :transform, :start | :stop]
  # [:org_garden, :watcher, :file_changed]
  # [:org_garden, :quartz, :started | :stopped]
end

5.2 Add telemetry calls to modules

In export.ex:

def export_file(orgfile, notes_dir, output_dir) do
  start_time = System.monotonic_time()
  Telemetry.export_start(%{file: orgfile})
  
  result = do_export(orgfile, notes_dir, output_dir)
  
  duration = System.monotonic_time() - start_time
  Telemetry.export_stop(%{file: orgfile}, %{duration: duration})
  
  result
end

5.3 Replace `IO.puts` with `Logger`

In cli.ex, watcher.ex:

IO.puts("==> ...") → Logger.info("...")
Keep IO.puts only for direct user output in CLI mode (non-service)

Phase 6: Mix Release

6.1 Update `mix.exs`

def project do
  [
    app: :org_garden,
    version: "0.1.0",
    elixir: "~> 1.17",
    start_permanent: Mix.env() == :prod,
    deps: deps(),
    escript: escript(),  # Keep for compatibility
    releases: releases()
  ]
end

defp releases do
  [
    org_garden: [
      include_executables_for: [:unix],
      applications: [runtime_tools: :permanent],
      steps: [:assemble, :tar]
    ]
  ]
end

6.2 Create `rel/env.sh.eex`

#!/bin/sh
export RELEASE_DISTRIBUTION=none
export RELEASE_NODE=org_garden

# Forward signals for graceful shutdown
export ERL_AFLAGS="-kernel shell_history enabled"

6.3 Create `rel/overlays/bin/org-garden`

#!/bin/sh
set -e

SELF=$(readlink -f "$0" 2>/dev/null || realpath "$0")
RELEASE_ROOT=$(dirname "$(dirname "$SELF")")

usage() {
  echo "Usage: org-garden <command> [options]"
  echo ""
  echo "Commands:"
  echo "  serve <notes-dir>    Start development server (long-running)"
  echo "  build <notes-dir>    Build static site (one-shot)"
  echo "  export <notes-dir>   Export org to markdown (one-shot)"
  echo "  daemon               Start as background daemon"
  echo "  stop                 Stop running daemon"
  echo "  remote               Connect to running instance"
  echo ""
}

case "${1:-}" in
  serve)
    shift
    exec "$RELEASE_ROOT/bin/org_garden" start -- "$@"
    ;;
  build|export)
    CMD="$1"
    shift
    exec "$RELEASE_ROOT/bin/org_garden" eval "OrgGarden.CLI.main([\"$CMD\" | System.argv()])" -- "$@"
    ;;
  daemon|stop|remote|pid|restart)
    exec "$RELEASE_ROOT/bin/org_garden" "$@"
    ;;
  -h|--help|help|"")
    usage
    ;;
  *)
    echo "Unknown command: $1"
    usage
    exit 1
    ;;
esac

Phase 7: NixOS Module

7.1 Create `nix/module.nix`

{ config, lib, pkgs, ... }:

let
  cfg = config.services.org-garden;
  pkg = config.services.org-garden.package;
in {
  options.services.org-garden = {
    enable = lib.mkEnableOption "org-garden publishing service";
    
    package = lib.mkOption {
      type = lib.types.package;
      description = "The org-garden package to use";
    };
    
    notesDir = lib.mkOption {
      type = lib.types.path;
      description = "Path to org-roam notes directory";
    };
    
    outputDir = lib.mkOption {
      type = lib.types.path;
      default = "/var/lib/org-garden";
      description = "Output directory for generated content";
    };
    
    port = lib.mkOption {
      type = lib.types.port;
      default = 8080;
      description = "HTTP server port";
    };
    
    wsPort = lib.mkOption {
      type = lib.types.port;
      default = 3001;
      description = "WebSocket hot reload port";
    };
    
    healthPort = lib.mkOption {
      type = lib.types.port;
      default = 9090;
      description = "Health check endpoint port";
    };
    
    zoteroUrl = lib.mkOption {
      type = lib.types.str;
      default = "http://localhost:23119";
      description = "Zotero Better BibTeX URL";
    };
    
    bibtexFile = lib.mkOption {
      type = lib.types.nullOr lib.types.path;
      default = null;
      description = "Path to fallback BibTeX file";
    };
    
    citationMode = lib.mkOption {
      type = lib.types.enum [ "silent" "warn" "strict" ];
      default = "warn";
      description = "Citation resolution failure mode";
    };
    
    user = lib.mkOption {
      type = lib.types.str;
      default = "org-garden";
      description = "User to run the service as";
    };
    
    group = lib.mkOption {
      type = lib.types.str;
      default = "org-garden";
      description = "Group to run the service as";
    };
  };

  config = lib.mkIf cfg.enable {
    users.users.${cfg.user} = {
      isSystemUser = true;
      group = cfg.group;
      home = cfg.outputDir;
    };
    
    users.groups.${cfg.group} = {};

    systemd.services.org-garden = {
      description = "Org-Garden Publishing Service";
      wantedBy = [ "multi-user.target" ];
      after = [ "network.target" ];
      
      environment = {
        NOTES_DIR = toString cfg.notesDir;
        OUTPUT_DIR = cfg.outputDir;
        PORT = toString cfg.port;
        WS_PORT = toString cfg.wsPort;
        HEALTH_PORT = toString cfg.healthPort;
        ZOTERO_URL = cfg.zoteroUrl;
        CITATION_MODE = cfg.citationMode;
      } // lib.optionalAttrs (cfg.bibtexFile != null) {
        BIBTEX_FILE = toString cfg.bibtexFile;
      };
      
      serviceConfig = {
        Type = "exec";
        ExecStart = "${pkg}/bin/org-garden serve";
        Restart = "on-failure";
        RestartSec = 5;
        
        # Directories
        StateDirectory = "org-garden";
        WorkingDirectory = cfg.outputDir;
        
        # Hardening
        User = cfg.user;
        Group = cfg.group;
        NoNewPrivileges = true;
        ProtectSystem = "strict";
        ProtectHome = "read-only";
        ReadWritePaths = [ cfg.outputDir ];
        ReadOnlyPaths = [ cfg.notesDir ];
        PrivateTmp = true;
      };
    };
  };
}

7.2 Update `flake.nix`

Add to outputs:

nixosModules.default = import ./nix/module.nix;

Update orgGardenApp to build as release instead of escript (optional, can keep both).

File Summary

New Files

File	Purpose
`lib/org_garden/server.ex`	Service mode lifecycle management
`lib/org_garden/config.ex`	Centralized configuration
`lib/org_garden/health.ex`	Health check HTTP endpoints
`lib/org_garden/telemetry.ex`	Telemetry event helpers
`config/config.exs`	Build-time config defaults
`config/runtime.exs`	Runtime config from env vars
`rel/env.sh.eex`	Release environment setup
`rel/overlays/bin/org-garden`	Unified CLI entry point
`nix/module.nix`	NixOS service module

Modified Files

File	Changes
`lib/org_garden/application.ex`	Add Registry, DynamicSupervisor, Health
`lib/org_garden/cli.ex`	Use Server module, Config
`lib/org_garden/supervisor.ex`	Minor: use Registry for naming
`lib/org_garden/quartz.ex`	Graceful shutdown, Config
`lib/org_garden/watcher.ex`	Drain period, telemetry, Logger
`lib/org_garden/export.ex`	Telemetry events
`mix.exs`	Add deps, releases config
`flake.nix`	Add nixosModules output

Implementation Order

Phase 2: Configuration — Foundation for all other phases
Phase 1: Supervision Tree — Core structural change
Phase 3: Graceful Shutdown — Builds on Phase 1
Phase 5: Observability — Independent, can be done in parallel
Phase 4: Health Checks — Depends on Phase 1 & 2
Phase 6: Mix Release — After code changes are stable
Phase 7: NixOS Module — Final, depends on release

Questions

Health check HTTP server: Should it always run, or only in serve mode? (I'm thinking always, so systemd can probe even during startup)
Telemetry consumers: Should we add a simple Logger-based telemetry handler that logs timings, or leave telemetry events for future Prometheus/metrics integration?
Should I proceed with implementation?

User (2026-02-21 20:09:01)

Always is fine. 2. Keep it simply for now. 3. Proceed.

Agent (2026-02-21 20:09:03)

I'll start implementing the improvements. Let me begin with Phase 2 (Configuration) as it's the foundation, then proceed through the phases.

Tool Call [completed]: todowrite

Tool: other Timestamp: 2026-02-21 20:09:09

[
  {
    "content": "Phase 2: Create config/config.exs with defaults",
    "status": "in_progress",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create config/runtime.exs for env vars",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create lib/org_garden/config.ex module",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 1: Refactor application.ex with DynamicSupervisor",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 1: Create lib/org_garden/server.ex",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 1: Update cli.ex to use Server module",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update quartz.ex for graceful shutdown",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update watcher.ex with drain period",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 5: Create lib/org_garden/telemetry.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 5: Add telemetry calls to export.ex and watcher.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Add bandit/plug deps to mix.exs",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Create lib/org_garden/health.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Add releases config to mix.exs",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/env.sh.eex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/overlays/bin/org-garden",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 7: Create nix/module.nix",
    "status": "pending",
    "priority": "low"
  },
  {
    "content": "Phase 7: Update flake.nix with nixosModules",
    "status": "pending",
    "priority": "low"
  }
]

Tool Call [completed]: mkdir -p config

Tool: execute Timestamp: 2026-02-21 20:09:12

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:09:17

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,18 @@
+import Config
+
+# Default configuration values
+# These are overridden by config/runtime.exs in releases
+
+config :org_garden,
+  zotero_url: "http://localhost:23119",
+  citation_mode: :warn,
+  http_port: 8080,
+  ws_port: 3001,
+  health_port: 9090
+
+config :logger, :console,
+  format: "$time $metadata[$level] $message\n",
+  metadata: [:module]
+
+# Import environment specific config
+import_config "#{config_env()}.exs"

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:09:20

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,4 @@
+import Config
+
+# Development-specific configuration
+config :logger, level: :debug

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:09:23

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,6 @@
+import Config
+
+# Production-specific configuration
+# Most config comes from runtime.exs via environment variables
+
+config :logger, level: :info

Tool Call [completed]: write

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Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,4 @@
+import Config
+
+# Test-specific configuration
+config :logger, level: :warning

Tool Call [completed]: todowrite

Tool: other Timestamp: 2026-02-21 20:09:36

[
  {
    "content": "Phase 2: Create config/config.exs with defaults",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create config/runtime.exs for env vars",
    "status": "in_progress",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create lib/org_garden/config.ex module",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 1: Refactor application.ex with DynamicSupervisor",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 1: Create lib/org_garden/server.ex",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 1: Update cli.ex to use Server module",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update quartz.ex for graceful shutdown",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update watcher.ex with drain period",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 5: Create lib/org_garden/telemetry.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 5: Add telemetry calls to export.ex and watcher.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Add bandit/plug deps to mix.exs",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Create lib/org_garden/health.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Add releases config to mix.exs",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/env.sh.eex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/overlays/bin/org-garden",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 7: Create nix/module.nix",
    "status": "pending",
    "priority": "low"
  },
  {
    "content": "Phase 7: Update flake.nix with nixosModules",
    "status": "pending",
    "priority": "low"
  }
]

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:09:45

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,42 @@
+import Config
+
+# Runtime configuration from environment variables
+# This file is executed at runtime (not compile time)
+
+defmodule RuntimeConfig do
+  def parse_int(nil, default), do: default
+  def parse_int(val, _default) when is_integer(val), do: val
+
+  def parse_int(val, default) when is_binary(val) do
+    case Integer.parse(val) do
+      {int, ""} -> int
+      _ -> default
+    end
+  end
+
+  def parse_citation_mode("silent"), do: :silent
+  def parse_citation_mode("strict"), do: :strict
+  def parse_citation_mode(_), do: :warn
+end
+
+# Core paths
+if quartz_path = System.get_env("QUARTZ_PATH") do
+  config :org_garden, quartz_path: quartz_path
+end
+
+config :org_garden,
+  node_path: System.get_env("NODE_PATH", "node"),
+  notes_dir: System.get_env("NOTES_DIR"),
+  output_dir: System.get_env("OUTPUT_DIR")
+
+# Citation configuration
+config :org_garden,
+  zotero_url: System.get_env("ZOTERO_URL", "http://localhost:23119"),
+  bibtex_file: System.get_env("BIBTEX_FILE"),
+  citation_mode: RuntimeConfig.parse_citation_mode(System.get_env("CITATION_MODE"))
+
+# Server ports
+config :org_garden,
+  http_port: RuntimeConfig.parse_int(System.get_env("PORT"), 8080),
+  ws_port: RuntimeConfig.parse_int(System.get_env("WS_PORT"), 3001),
+  health_port: RuntimeConfig.parse_int(System.get_env("HEALTH_PORT"), 9090)

Tool Call [completed]: todowrite

Tool: other Timestamp: 2026-02-21 20:09:52

[
  {
    "content": "Phase 2: Create config/config.exs with defaults",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create config/runtime.exs for env vars",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create lib/org_garden/config.ex module",
    "status": "in_progress",
    "priority": "high"
  },
  {
    "content": "Phase 1: Refactor application.ex with DynamicSupervisor",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 1: Create lib/org_garden/server.ex",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 1: Update cli.ex to use Server module",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update quartz.ex for graceful shutdown",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update watcher.ex with drain period",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 5: Create lib/org_garden/telemetry.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 5: Add telemetry calls to export.ex and watcher.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Add bandit/plug deps to mix.exs",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Create lib/org_garden/health.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Add releases config to mix.exs",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/env.sh.eex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/overlays/bin/org-garden",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 7: Create nix/module.nix",
    "status": "pending",
    "priority": "low"
  },
  {
    "content": "Phase 7: Update flake.nix with nixosModules",
    "status": "pending",
    "priority": "low"
  }
]

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:10:05

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,98 @@
+defmodule OrgGarden.Config do
+  @moduledoc """
+  Centralized configuration access with validation.
+
+  Provides a unified interface for accessing configuration values,
+  with support for defaults and required value validation.
+
+  ## Usage
+
+      OrgGarden.Config.get(:http_port)
+      #=> 8080
+
+      OrgGarden.Config.get!(:quartz_path)
+      #=> "/path/to/quartz" or raises if not set
+
+      OrgGarden.Config.pipeline_opts()
+      #=> %{zotero_url: "...", bibtex_file: nil, citation_mode: :warn}
+  """
+
+  @doc """
+  Get a configuration value with an optional default.
+  """
+  def get(key, default \\ nil) do
+    Application.get_env(:org_garden, key, default)
+  end
+
+  @doc """
+  Get a required configuration value. Raises if not set.
+  """
+  def get!(key) do
+    case Application.get_env(:org_garden, key) do
+      nil -> raise ArgumentError, "Missing required configuration: #{key}"
+      value -> value
+    end
+  end
+
+  @doc """
+  Build pipeline options map for transforms.
+  """
+  def pipeline_opts do
+    %{
+      zotero_url: get(:zotero_url, "http://localhost:23119"),
+      bibtex_file: get(:bibtex_file),
+      citation_mode: get(:citation_mode, :warn)
+    }
+  end
+
+  @doc """
+  Validate that all required configuration is present.
+  Returns :ok or {:error, reasons}.
+  """
+  def validate do
+    errors =
+      []
+      |> validate_quartz_path()
+      |> validate_citation_mode()
+
+    case errors do
+      [] -> :ok
+      errors -> {:error, errors}
+    end
+  end
+
+  @doc """
+  Validate configuration and raise on errors.
+  """
+  def validate! do
+    case validate() do
+      :ok -> :ok
+      {:error, errors} -> raise "Configuration errors: #{inspect(errors)}"
+    end
+  end
+
+  # Private validation helpers
+
+  defp validate_quartz_path(errors) do
+    case get(:quartz_path) do
+      nil ->
+        errors
+
+      path ->
+        cli_path = Path.join(path, "quartz/bootstrap-cli.mjs")
+
+        if File.exists?(cli_path) do
+          errors
+        else
+          [{:quartz_path, "bootstrap-cli.mjs not found at #{cli_path}"} | errors]
+        end
+    end
+  end
+
+  defp validate_citation_mode(errors) do
+    case get(:citation_mode) do
+      mode when mode in [:silent, :warn, :strict] -> errors
+      other -> [{:citation_mode, "Invalid citation mode: #{inspect(other)}"} | errors]
+    end
+  end
+end

Tool Call [completed]: todowrite

Tool: other Timestamp: 2026-02-21 20:10:13

[
  {
    "content": "Phase 2: Create config/config.exs with defaults",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create config/runtime.exs for env vars",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create lib/org_garden/config.ex module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Refactor application.ex with DynamicSupervisor",
    "status": "in_progress",
    "priority": "high"
  },
  {
    "content": "Phase 1: Create lib/org_garden/server.ex",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 1: Update cli.ex to use Server module",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update quartz.ex for graceful shutdown",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update watcher.ex with drain period",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 5: Create lib/org_garden/telemetry.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 5: Add telemetry calls to export.ex and watcher.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Add bandit/plug deps to mix.exs",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Create lib/org_garden/health.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Add releases config to mix.exs",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/env.sh.eex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/overlays/bin/org-garden",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 7: Create nix/module.nix",
    "status": "pending",
    "priority": "low"
  },
  {
    "content": "Phase 7: Update flake.nix with nixosModules",
    "status": "pending",
    "priority": "low"
  }
]

Agent (2026-02-21 20:10:14)

Now let me refactor application.ex:

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:10:21

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,39 @@
+defmodule OrgGarden.Application do
+  @moduledoc """
+  OTP Application for org-garden.
+
+  Starts core infrastructure services:
+  - Finch HTTP client pool
+  - Process registry for named lookups
+  - DynamicSupervisor for runtime-started services
+  - Health check HTTP server
+
+  Service-mode components (Watcher, Quartz) are started dynamically
+  via OrgGarden.Server when running in serve mode.
+  """
+  use Application
+
+  @impl true
+  def start(_type, _args) do
+    children = [
+      # HTTP client pool for Zotero/external requests
+      {Finch, name: OrgGarden.Finch},
+
+      # Process registry for named lookups
+      {Registry, keys: :unique, name: OrgGarden.Registry},
+
+      # Dynamic supervisor for serve mode components
+      {DynamicSupervisor, name: OrgGarden.DynamicSupervisor, strategy: :one_for_one},
+
+      # Health check HTTP server
+      {Bandit, plug: OrgGarden.Health, port: health_port(), scheme: :http}
+    ]
+
+    opts = [strategy: :one_for_one, name: OrgGarden.AppSupervisor]
+    Supervisor.start_link(children, opts)
+  end
+
+  defp health_port do
+    Application.get_env(:org_garden, :health_port, 9090)
+  end
+end

Tool Call [completed]: todowrite

Tool: other Timestamp: 2026-02-21 20:10:28

[
  {
    "content": "Phase 2: Create config/config.exs with defaults",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create config/runtime.exs for env vars",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create lib/org_garden/config.ex module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Refactor application.ex with DynamicSupervisor",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Create lib/org_garden/server.ex",
    "status": "in_progress",
    "priority": "high"
  },
  {
    "content": "Phase 1: Update cli.ex to use Server module",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update quartz.ex for graceful shutdown",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update watcher.ex with drain period",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 5: Create lib/org_garden/telemetry.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 5: Add telemetry calls to export.ex and watcher.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Add bandit/plug deps to mix.exs",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Create lib/org_garden/health.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Add releases config to mix.exs",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/env.sh.eex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/overlays/bin/org-garden",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 7: Create nix/module.nix",
    "status": "pending",
    "priority": "low"
  },
  {
    "content": "Phase 7: Update flake.nix with nixosModules",
    "status": "pending",
    "priority": "low"
  }
]

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:10:52

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,212 @@
+defmodule OrgGarden.Server do
+  @moduledoc """
+  Manages the serve mode lifecycle.
+
+  This GenServer encapsulates the full serve mode workflow:
+  1. Run initial export pipeline
+  2. Start supervised Watcher + Quartz under DynamicSupervisor
+  3. Handle graceful shutdown on termination
+
+  ## Usage
+
+      # Start the server (blocks until stopped)
+      {:ok, pid} = OrgGarden.Server.start_link(
+        notes_dir: "/path/to/notes",
+        output_dir: "/path/to/output"
+      )
+
+      # Stop gracefully
+      OrgGarden.Server.stop()
+  """
+
+  use GenServer
+
+  require Logger
+
+  alias OrgGarden.Config
+
+  @transforms [OrgGarden.Transforms.Citations]
+
+  # -------------------------------------------------------------------
+  # Client API
+  # -------------------------------------------------------------------
+
+  @doc """
+  Start the serve mode server.
+
+  ## Options
+
+    * `:notes_dir` — path to org-roam notes (required)
+    * `:output_dir` — output base directory (required)
+    * `:content_dir` — markdown output directory (default: output_dir/content)
+    * `:port` — HTTP server port (default: from config)
+    * `:ws_port` — WebSocket port (default: from config)
+  """
+  def start_link(opts) do
+    GenServer.start_link(__MODULE__, opts, name: __MODULE__)
+  end
+
+  @doc """
+  Stop the server gracefully.
+  """
+  def stop(timeout \\ 10_000) do
+    GenServer.stop(__MODULE__, :normal, timeout)
+  end
+
+  @doc """
+  Check if the server is running.
+  """
+  def running? do
+    Process.whereis(__MODULE__) != nil
+  end
+
+  # -------------------------------------------------------------------
+  # GenServer callbacks
+  # -------------------------------------------------------------------
+
+  @impl true
+  def init(opts) do
+    Process.flag(:trap_exit, true)
+
+    notes_dir = Keyword.fetch!(opts, :notes_dir)
+    output_dir = Keyword.fetch!(opts, :output_dir)
+    content_dir = Keyword.get(opts, :content_dir, Path.join(output_dir, "content"))
+    http_port = Keyword.get(opts, :port, Config.get(:http_port, 8080))
+    ws_port = Keyword.get(opts, :ws_port, Config.get(:ws_port, 3001))
+
+    pipeline_opts = Config.pipeline_opts()
+
+    state = %{
+      notes_dir: notes_dir,
+      output_dir: output_dir,
+      content_dir: content_dir,
+      pipeline_opts: pipeline_opts,
+      http_port: http_port,
+      ws_port: ws_port,
+      supervisor_pid: nil
+    }
+
+    # Run initial pipeline synchronously
+    case run_initial_pipeline(state) do
+      :ok ->
+        # Start supervised components
+        case start_supervisor(state) do
+          {:ok, sup_pid} ->
+            Logger.info("Server started on http://localhost:#{http_port}")
+            Logger.info("Watching #{notes_dir} for changes")
+            {:ok, %{state | supervisor_pid: sup_pid}}
+
+          {:error, reason} ->
+            {:stop, reason}
+        end
+
+      {:error, reason} ->
+        {:stop, reason}
+    end
+  end
+
+  @impl true
+  def handle_info({:EXIT, pid, reason}, %{supervisor_pid: pid} = state) do
+    Logger.error("Supervisor exited: #{inspect(reason)}")
+    {:stop, {:supervisor_exit, reason}, state}
+  end
+
+  @impl true
+  def handle_info({:EXIT, _pid, reason}, state) do
+    Logger.warning("Linked process exited: #{inspect(reason)}")
+    {:noreply, state}
+  end
+
+  @impl true
+  def terminate(reason, state) do
+    Logger.info("Server shutting down: #{inspect(reason)}")
+
+    if state.supervisor_pid do
+      # Stop the supervisor gracefully
+      DynamicSupervisor.terminate_child(OrgGarden.DynamicSupervisor, state.supervisor_pid)
+    end
+
+    :ok
+  end
+
+  # -------------------------------------------------------------------
+  # Private functions
+  # -------------------------------------------------------------------
+
+  defp run_initial_pipeline(state) do
+    %{
+      notes_dir: notes_dir,
+      output_dir: output_dir,
+      content_dir: content_dir,
+      pipeline_opts: pipeline_opts
+    } = state
+
+    Logger.info("Running initial export pipeline...")
+
+    # Wipe content directory
+    wipe(content_dir)
+
+    # Export all org files
+    case OrgGarden.Export.export_all(notes_dir, output_dir) do
+      {:ok, 0} ->
+        Logger.warning("No .org files found in #{notes_dir}")
+        :ok
+
+      {:ok, count} ->
+        Logger.info("Exported #{count} file(s)")
+
+        # Run transforms
+        {:ok, stats} = OrgGarden.run(content_dir, @transforms, pipeline_opts)
+
+        Enum.each(stats, fn {mod, c} ->
+          Logger.info("#{inspect(mod)}: #{c} file(s) modified")
+        end)
+
+        # Generate index
+        OrgGarden.Index.generate(content_dir)
+        :ok
+
+      {:error, failures} ->
+        Logger.error("Failed to export #{length(failures)} file(s)")
+        {:error, {:export_failed, failures}}
+    end
+  end
+
+  defp start_supervisor(state) do
+    %{
+      notes_dir: notes_dir,
+      output_dir: output_dir,
+      content_dir: content_dir,
+      pipeline_opts: pipeline_opts,
+      http_port: http_port,
+      ws_port: ws_port
+    } = state
+
+    child_spec = {
+      OrgGarden.Supervisor,
+      [
+        notes_dir: notes_dir,
+        output_dir: output_dir,
+        content_dir: content_dir,
+        pipeline_opts: pipeline_opts,
+        transforms: @transforms,
+        port: http_port,
+        ws_port: ws_port
+      ]
+    }
+
+    DynamicSupervisor.start_child(OrgGarden.DynamicSupervisor, child_spec)
+  end
+
+  defp wipe(content_dir) do
+    Logger.info("Wiping #{content_dir}")
+    File.mkdir_p!(content_dir)
+
+    content_dir
+    |> File.ls!()
+    |> Enum.reject(&(&1 == ".gitkeep"))
+    |> Enum.each(fn entry ->
+      Path.join(content_dir, entry) |> File.rm_rf!()
+    end)
+  end
+end

Agent (2026-02-21 20:10:54)

Now let me create the Health module since application.ex depends on it, then update mix.exs with the new dependencies:

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:11:04

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,95 @@
+defmodule OrgGarden.Health do
+  @moduledoc """
+  Health check HTTP endpoints.
+
+  Provides liveness and readiness probes for systemd/kubernetes health checks.
+
+  ## Endpoints
+
+    * `GET /health/live` — Always returns 200 if the process is alive
+    * `GET /health/ready` — Returns 200 if all components are ready, 503 otherwise
+    * `GET /health` — Returns JSON status of all components
+  """
+
+  use Plug.Router
+
+  plug(:match)
+  plug(:dispatch)
+
+  @doc """
+  Liveness probe — is the process alive?
+  """
+  get "/health/live" do
+    send_resp(conn, 200, "ok")
+  end
+
+  @doc """
+  Readiness probe — are all components ready to serve?
+  """
+  get "/health/ready" do
+    checks = run_checks()
+    all_healthy = Enum.all?(checks, fn {_name, status} -> status == :ok end)
+
+    if all_healthy do
+      send_resp(conn, 200, "ready")
+    else
+      send_resp(conn, 503, "not ready")
+    end
+  end
+
+  @doc """
+  Full health status as JSON.
+  """
+  get "/health" do
+    checks = run_checks()
+    all_healthy = Enum.all?(checks, fn {_name, status} -> status == :ok end)
+
+    status =
+      if all_healthy do
+        "healthy"
+      else
+        "degraded"
+      end
+
+    body =
+      Jason.encode!(%{
+        status: status,
+        checks:
+          Map.new(checks, fn {name, status} ->
+            {name, Atom.to_string(status)}
+          end)
+      })
+
+    conn
+    |> put_resp_content_type("application/json")
+    |> send_resp(if(all_healthy, do: 200, else: 503), body)
+  end
+
+  match _ do
+    send_resp(conn, 404, "not found")
+  end
+
+  # -------------------------------------------------------------------
+  # Health checks
+  # -------------------------------------------------------------------
+
+  defp run_checks do
+    [
+      {:server, check_server()},
+      {:watcher, check_watcher()},
+      {:quartz, check_quartz()}
+    ]
+  end
+
+  defp check_server do
+    if Process.whereis(OrgGarden.Server), do: :ok, else: :not_running
+  end
+
+  defp check_watcher do
+    if Process.whereis(OrgGarden.Watcher), do: :ok, else: :not_running
+  end
+
+  defp check_quartz do
+    if Process.whereis(OrgGarden.Quartz), do: :ok, else: :not_running
+  end
+end

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-21 20:11:07

<path>/home/ignaciobll/code/org-garden/mix.exs</path>
<type>file</type>
<content>1: defmodule OrgGarden.MixProject do
2:   use Mix.Project
3: 
4:   def project do
5:     [
6:       app: :org_garden,
7:       version: "0.1.0",
8:       elixir: "~> 1.17",
9:       start_permanent: Mix.env() == :prod,
10:       deps: deps(),
11:       escript: escript()
12:     ]
13:   end
14: 
15:   def application do
16:     [
17:       extra_applications: [:logger],
18:       mod: {OrgGarden.Application, []}
19:     ]
20:   end
21: 
22:   defp escript do
23:     [main_module: OrgGarden.CLI]
24:   end
25: 
26:   defp deps do
27:     [
28:       {:finch, "~> 0.19"},
29:       {:req, "~> 0.5"},
30:       {:jason, "~> 1.4"},
31:       {:file_system, "~> 1.0"}
32:     ]
33:   end
34: end
35: 

(End of file - total 35 lines)
</content>

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:11:14

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,50 @@
+defmodule OrgGarden.MixProject do
+  use Mix.Project
+
+  def project do
+    [
+      app: :org_garden,
+      version: "0.1.0",
+      elixir: "~> 1.17",
+      start_permanent: Mix.env() == :prod,
+      deps: deps(),
+      escript: escript(),
+      releases: releases()
+    ]
+  end
+
+  def application do
+    [
+      extra_applications: [:logger],
+      mod: {OrgGarden.Application, []}
+    ]
+  end
+
+  defp escript do
+    [main_module: OrgGarden.CLI]
+  end
+
+  defp releases do
+    [
+      org_garden: [
+        include_executables_for: [:unix],
+        applications: [runtime_tools: :permanent],
+        steps: [:assemble, :tar]
+      ]
+    ]
+  end
+
+  defp deps do
+    [
+      {:finch, "~> 0.19"},
+      {:req, "~> 0.5"},
+      {:jason, "~> 1.4"},
+      {:file_system, "~> 1.0"},
+      # Health check HTTP server
+      {:bandit, "~> 1.0"},
+      {:plug, "~> 1.15"},
+      # Telemetry
+      {:telemetry, "~> 1.0"}
+    ]
+  end
+end

Tool Call [completed]: todowrite

Tool: other Timestamp: 2026-02-21 20:11:25

[
  {
    "content": "Phase 2: Create config/config.exs with defaults",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create config/runtime.exs for env vars",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create lib/org_garden/config.ex module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Refactor application.ex with DynamicSupervisor",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Create lib/org_garden/server.ex",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Update cli.ex to use Server module",
    "status": "in_progress",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update quartz.ex for graceful shutdown",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update watcher.ex with drain period",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 5: Create lib/org_garden/telemetry.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 5: Add telemetry calls to export.ex and watcher.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Add bandit/plug deps to mix.exs",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Create lib/org_garden/health.ex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Add releases config to mix.exs",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/env.sh.eex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/overlays/bin/org-garden",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 7: Create nix/module.nix",
    "status": "pending",
    "priority": "low"
  },
  {
    "content": "Phase 7: Update flake.nix with nixosModules",
    "status": "pending",
    "priority": "low"
  }
]

Agent (2026-02-21 20:11:27)

Now let me update cli.ex to use the new Server module:

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:12:13

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,382 @@
+defmodule OrgGarden.CLI do
+  @moduledoc """
+  Escript entry point for the org-garden pipeline.
+
+  ## Commands
+
+      org-garden serve <notes-dir> [--port 8080] [--ws-port 3001]
+      org-garden build <notes-dir> [--output <path>]
+      org-garden export <notes-dir> [--watch]
+
+  ### serve
+  Development server with watch + live reload. Starts both the org→md
+  watcher and Quartz in serve mode.
+
+  ### build
+  One-shot build for CI/production. Exports org files, runs transforms,
+  then builds static site with Quartz.
+
+  ### export
+  Just export org→md (current pipeline behavior). Use --watch for
+  incremental re-export on file changes.
+
+  ## Arguments
+
+    notes-dir          Path to the directory containing `.org` notes (required).
+                       Also accepts the `NOTES_DIR` env var.
+
+  ## Options
+
+    --output <path>    Output root directory (used as ox-hugo base dir).
+                       Defaults to the `OUTPUT_DIR` env var, or the current
+                       working directory.
+    --content-dir <p>  Output directory for exported Markdown. Defaults to
+                       `<output>/content`.
+    --port <n>         HTTP server port (default: 8080). Only for `serve`.
+    --ws-port <n>      WebSocket hot reload port (default: 3001). Only for `serve`.
+    --watch            After initial batch, watch notes-dir for changes and
+                       incrementally re-export affected files. Only for `export`.
+
+  ## Environment Variables
+
+    BIBTEX_FILE        Path to a `.bib` file used as citation fallback.
+    ZOTERO_URL         Zotero Better BibTeX base URL (default: http://localhost:23119).
+    CITATION_MODE      silent | warn (default) | strict.
+    QUARTZ_PATH        Path to quartz directory (required for serve/build).
+    NODE_PATH          Node.js executable (default: node).
+  """
+
+  require Logger
+
+  alias OrgGarden.Config
+
+  @transforms [OrgGarden.Transforms.Citations]
+
+  def main(argv) do
+    Application.ensure_all_started(:org_garden)
+
+    case argv do
+      ["serve" | rest] -> handle_serve(rest)
+      ["build" | rest] -> handle_build(rest)
+      ["export" | rest] -> handle_export(rest)
+      # Legacy: treat bare args as export command for backward compatibility
+      [_ | _] -> handle_export(argv)
+      _ -> abort("Usage: org-garden <serve|build|export> <notes-dir> [options]")
+    end
+  end
+
+  # ---------------------------------------------------------------------------
+  # Command: serve
+  # ---------------------------------------------------------------------------
+
+  def handle_serve(argv) do
+    require_quartz_env()
+    {notes_dir, output_dir, content_dir, opts} = parse_serve_args(argv)
+
+    IO.puts("==> Starting development server...")
+
+    case OrgGarden.Server.start_link(
+           notes_dir: notes_dir,
+           output_dir: output_dir,
+           content_dir: content_dir,
+           port: opts[:port],
+           ws_port: opts[:ws_port]
+         ) do
+      {:ok, pid} ->
+        IO.puts("==> Server running at http://localhost:#{opts[:port] || Config.get(:http_port, 8080)}")
+        IO.puts("==> Watching #{notes_dir} for changes (Ctrl+C to stop)")
+
+        # Wait for server to exit
+        ref = Process.monitor(pid)
+
+        receive do
+          {:DOWN, ^ref, :process, ^pid, reason} ->
+            case reason do
+              :normal -> :ok
+              :shutdown -> :ok
+              {:shutdown, _} -> :ok
+              _ -> abort("Server crashed: #{inspect(reason)}")
+            end
+        end
+
+      {:error, reason} ->
+        abort("Failed to start server: #{inspect(reason)}")
+    end
+  end
+
+  defp parse_serve_args(argv) do
+    {opts, positional, _invalid} =
+      OptionParser.parse(argv,
+        strict: [
+          output: :string,
+          content_dir: :string,
+          port: :integer,
+          ws_port: :integer
+        ]
+      )
+
+    notes_dir = extract_notes_dir(positional, "serve")
+    output_dir = extract_output_dir(opts)
+    content_dir = extract_content_dir(opts, output_dir)
+
+    {notes_dir, output_dir, content_dir, opts}
+  end
+
+  # ---------------------------------------------------------------------------
+  # Command: build
+  # ---------------------------------------------------------------------------
+
+  def handle_build(argv) do
+    quartz_path = require_quartz_env()
+    {notes_dir, output_dir, content_dir, _opts} = parse_build_args(argv)
+    pipeline_opts = Config.pipeline_opts()
+
+    # Full batch export
+    wipe(content_dir)
+    export_all(notes_dir, output_dir)
+    run_pipeline(content_dir, pipeline_opts)
+    generate_index(content_dir)
+
+    node_path = Config.get(:node_path, "node")
+
+    IO.puts("==> Building static site with Quartz...")
+
+    {output, status} =
+      System.cmd(
+        node_path,
+        [
+          Path.join(quartz_path, "quartz/bootstrap-cli.mjs"),
+          "build",
+          "--directory",
+          content_dir,
+          "--output",
+          Path.join(output_dir, "public")
+        ],
+        cd: quartz_path,
+        stderr_to_stdout: true
+      )
+
+    IO.puts(output)
+
+    if status != 0 do
+      abort("Quartz build failed with status #{status}")
+    end
+
+    IO.puts("==> Build complete. Output: #{Path.join(output_dir, "public")}")
+  end
+
+  defp parse_build_args(argv) do
+    {opts, positional, _invalid} =
+      OptionParser.parse(argv,
+        strict: [output: :string, content_dir: :string]
+      )
+
+    notes_dir = extract_notes_dir(positional, "build")
+    output_dir = extract_output_dir(opts)
+    content_dir = extract_content_dir(opts, output_dir)
+
+    {notes_dir, output_dir, content_dir, opts}
+  end
+
+  # ---------------------------------------------------------------------------
+  # Command: export (original pipeline behavior)
+  # ---------------------------------------------------------------------------
+
+  def handle_export(argv) do
+    {notes_dir, output_dir, content_dir, watch?} = parse_export_args(argv)
+    pipeline_opts = Config.pipeline_opts()
+
+    # Phase 1-4: full batch export
+    wipe(content_dir)
+    export_all(notes_dir, output_dir)
+    run_pipeline(content_dir, pipeline_opts)
+    generate_index(content_dir)
+
+    md_count =
+      content_dir
+      |> Path.join("**/*.md")
+      |> Path.wildcard()
+      |> length()
+
+    IO.puts("==> Done. #{md_count} markdown files in #{content_dir}")
+
+    # Phase 5: optional watch mode
+    if watch? do
+      IO.puts("==> Watching #{notes_dir} for .org changes... (Ctrl+C to stop)")
+
+      {:ok, pid} =
+        DynamicSupervisor.start_child(
+          OrgGarden.DynamicSupervisor,
+          {OrgGarden.Watcher,
+           notes_dir: notes_dir,
+           output_dir: output_dir,
+           content_dir: content_dir,
+           pipeline_opts: pipeline_opts,
+           transforms: @transforms}
+        )
+
+      # Wait for watcher to exit
+      ref = Process.monitor(pid)
+
+      receive do
+        {:DOWN, ^ref, :process, ^pid, reason} ->
+          case reason do
+            :normal -> :ok
+            :shutdown -> :ok
+            {:shutdown, _} -> :ok
+            _ -> abort("Watcher crashed: #{inspect(reason)}")
+          end
+      end
+    end
+  end
+
+  defp parse_export_args(argv) do
+    {opts, positional, _invalid} =
+      OptionParser.parse(argv,
+        strict: [output: :string, content_dir: :string, watch: :boolean]
+      )
+
+    notes_dir = extract_notes_dir(positional, "export")
+    output_dir = extract_output_dir(opts)
+    content_dir = extract_content_dir(opts, output_dir)
+    watch? = Keyword.get(opts, :watch, false)
+
+    {notes_dir, output_dir, content_dir, watch?}
+  end
+
+  # ---------------------------------------------------------------------------
+  # Shared argument extraction
+  # ---------------------------------------------------------------------------
+
+  defp extract_notes_dir(positional, command) do
+    notes_dir =
+      case positional do
+        [dir | _] ->
+          dir
+
+        [] ->
+          Config.get(:notes_dir) ||
+            abort("Usage: org-garden #{command} <notes-dir> [options]")
+      end
+
+    notes_dir = Path.expand(notes_dir)
+
+    unless File.dir?(notes_dir) do
+      abort("Error: notes directory does not exist: #{notes_dir}")
+    end
+
+    notes_dir
+  end
+
+  defp extract_output_dir(opts) do
+    (opts[:output] || Config.get(:output_dir) || File.cwd!())
+    |> Path.expand()
+  end
+
+  defp extract_content_dir(opts, output_dir) do
+    (opts[:content_dir] || Path.join(output_dir, "content"))
+    |> Path.expand()
+  end
+
+  # ---------------------------------------------------------------------------
+  # Phase 1: Wipe content/
+  # ---------------------------------------------------------------------------
+
+  defp wipe(content_dir) do
+    IO.puts("==> Wiping #{content_dir}")
+    File.mkdir_p!(content_dir)
+
+    content_dir
+    |> File.ls!()
+    |> Enum.reject(&(&1 == ".gitkeep"))
+    |> Enum.each(fn entry ->
+      Path.join(content_dir, entry) |> File.rm_rf!()
+    end)
+  end
+
+  # ---------------------------------------------------------------------------
+  # Phase 2: Export org files via Emacs + ox-hugo
+  # ---------------------------------------------------------------------------
+
+  defp export_all(notes_dir, output_dir) do
+    IO.puts("==> Exporting org files from #{notes_dir}")
+
+    case OrgGarden.Export.export_all(notes_dir, output_dir) do
+      {:ok, 0} ->
+        IO.puts("No .org files found in #{notes_dir}")
+        System.halt(0)
+
+      {:ok, count} ->
+        IO.puts("  exported #{count} file(s)")
+
+      {:error, failures} ->
+        IO.puts(:stderr, "\nFailed to export #{length(failures)} file(s):")
+
+        Enum.each(failures, fn {f, {:error, reason}} ->
+          IO.puts(:stderr, "  #{f}: #{inspect(reason)}")
+        end)
+
+        System.halt(1)
+    end
+  end
+
+  # ---------------------------------------------------------------------------
+  # Phase 3: Markdown transformation pipeline
+  # ---------------------------------------------------------------------------
+
+  defp run_pipeline(content_dir, pipeline_opts) do
+    IO.puts("==> Running markdown pipeline")
+
+    {:ok, stats} = OrgGarden.run(content_dir, @transforms, pipeline_opts)
+
+    Enum.each(stats, fn {mod, count} ->
+      IO.puts("  #{inspect(mod)}: #{count} file(s) modified")
+    end)
+  end
+
+  # ---------------------------------------------------------------------------
+  # Phase 4: Generate default index.md if none was exported
+  # ---------------------------------------------------------------------------
+
+  defp generate_index(content_dir) do
+    IO.puts("==> Generating index")
+    OrgGarden.Index.generate(content_dir)
+  end
+
+  # ---------------------------------------------------------------------------
+  # Helpers
+  # ---------------------------------------------------------------------------
+
+  defp require_quartz_env do
+    case Config.get(:quartz_path) do
+      nil ->
+        abort("""
+        Error: QUARTZ_PATH environment variable not set.
+
+        The 'serve' and 'build' commands require Quartz to be available.
+
+        Use the wrapper scripts that set up the environment:
+          nix run .#notes -- <notes-dir>     # for serve
+          nix run .#build -- <notes-dir>     # for build
+
+        Or set QUARTZ_PATH manually to point to a quartz-org-roam checkout
+        with node_modules installed.
+
+        For export-only mode (no Quartz), use:
+          org-garden export <notes-dir> [--watch]
+        """)
+
+      path ->
+        unless File.exists?(Path.join(path, "quartz/bootstrap-cli.mjs")) do
+          abort("Error: QUARTZ_PATH=#{path} does not contain quartz/bootstrap-cli.mjs")
+        end
+
+        path
+    end
+  end
+
+  defp abort(message) do
+    IO.puts(:stderr, message)
+    System.halt(1)
+  end
+end

Tool Call [completed]: todowrite

Tool: other Timestamp: 2026-02-21 20:12:23

[
  {
    "content": "Phase 2: Create config/config.exs with defaults",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create config/runtime.exs for env vars",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create lib/org_garden/config.ex module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Refactor application.ex with DynamicSupervisor",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Create lib/org_garden/server.ex",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Update cli.ex to use Server module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update quartz.ex for graceful shutdown",
    "status": "in_progress",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update watcher.ex with drain period",
    "status": "pending",
    "priority": "high"
  },
  {
    "content": "Phase 5: Create lib/org_garden/telemetry.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 5: Add telemetry calls to export.ex and watcher.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Add bandit/plug deps to mix.exs",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Create lib/org_garden/health.ex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Add releases config to mix.exs",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/env.sh.eex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/overlays/bin/org-garden",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 7: Create nix/module.nix",
    "status": "pending",
    "priority": "low"
  },
  {
    "content": "Phase 7: Update flake.nix with nixosModules",
    "status": "pending",
    "priority": "low"
  }
]

Agent (2026-02-21 20:12:26)

Now let's update quartz.ex for graceful shutdown:

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:12:48

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,183 @@
+defmodule OrgGarden.Quartz do
+  @moduledoc """
+  Manages Quartz Node.js process as an Erlang Port.
+
+  Required environment:
+  - QUARTZ_PATH: path to quartz repo (with node_modules)
+  - NODE_PATH: path to node executable (default: "node")
+
+  Starts Quartz in serve mode (`npx quartz build --serve`) and forwards
+  all stdout/stderr output to the Logger with a `[quartz]` prefix.
+
+  If Quartz exits, this GenServer will stop, which triggers the supervisor
+  to restart the entire supervision tree (strategy: :one_for_all).
+  """
+  use GenServer
+
+  require Logger
+
+  alias OrgGarden.Config
+
+  @shutdown_timeout 5_000
+
+  defstruct [:port, :os_pid, :quartz_path, :content_dir, :http_port, :ws_port]
+
+  # -------------------------------------------------------------------
+  # Client API
+  # -------------------------------------------------------------------
+
+  @doc """
+  Start the Quartz process as a linked GenServer.
+
+  ## Options
+
+    * `:content_dir` — directory where markdown files are located (required)
+    * `:port`        — HTTP server port (default: 8080)
+    * `:ws_port`     — WebSocket hot reload port (default: 3001)
+  """
+  def start_link(opts) do
+    GenServer.start_link(__MODULE__, opts, name: __MODULE__)
+  end
+
+  @doc """
+  Check if Quartz is running.
+  """
+  def running? do
+    Process.whereis(__MODULE__) != nil
+  end
+
+  # -------------------------------------------------------------------
+  # GenServer callbacks
+  # -------------------------------------------------------------------
+
+  @impl true
+  def init(opts) do
+    Process.flag(:trap_exit, true)
+
+    quartz_path = Config.get!(:quartz_path)
+    node_path = Config.get(:node_path, "node")
+
+    content_dir = Keyword.fetch!(opts, :content_dir)
+    http_port = Keyword.get(opts, :port, Config.get(:http_port, 8080))
+    ws_port = Keyword.get(opts, :ws_port, Config.get(:ws_port, 3001))
+
+    cli_path = Path.join(quartz_path, "quartz/bootstrap-cli.mjs")
+
+    unless File.exists?(cli_path) do
+      raise "Quartz CLI not found at #{cli_path}. Check QUARTZ_PATH."
+    end
+
+    args = [
+      cli_path,
+      "build",
+      "--serve",
+      "--directory",
+      content_dir,
+      "--port",
+      to_string(http_port),
+      "--wsPort",
+      to_string(ws_port)
+    ]
+
+    Logger.info("[quartz] Starting: #{node_path} #{Enum.join(args, " ")}")
+    Logger.info("[quartz] Working directory: #{quartz_path}")
+
+    port =
+      Port.open({:spawn_executable, node_path}, [
+        :binary,
+        :exit_status,
+        :stderr_to_stdout,
+        args: args,
+        cd: quartz_path,
+        env: [{~c"NODE_NO_WARNINGS", ~c"1"}]
+      ])
+
+    # Get the OS process ID for graceful shutdown
+    {:os_pid, os_pid} = Port.info(port, :os_pid)
+
+    state = %__MODULE__{
+      port: port,
+      os_pid: os_pid,
+      quartz_path: quartz_path,
+      content_dir: content_dir,
+      http_port: http_port,
+      ws_port: ws_port
+    }
+
+    {:ok, state}
+  end
+
+  @impl true
+  def handle_info({port, {:data, data}}, %{port: port} = state) do
+    data
+    |> String.split("\n", trim: true)
+    |> Enum.each(&Logger.info("[quartz] #{&1}"))
+
+    {:noreply, state}
+  end
+
+  @impl true
+  def handle_info({port, {:exit_status, status}}, %{port: port} = state) do
+    Logger.error("[quartz] Process exited with status #{status}")
+    {:stop, {:quartz_exit, status}, %{state | port: nil, os_pid: nil}}
+  end
+
+  @impl true
+  def handle_info({:EXIT, port, reason}, %{port: port} = state) do
+    Logger.warning("[quartz] Port terminated: #{inspect(reason)}")
+    {:stop, {:port_exit, reason}, %{state | port: nil, os_pid: nil}}
+  end
+
+  @impl true
+  def terminate(_reason, %{os_pid: nil}) do
+    # Process already exited
+    :ok
+  end
+
+  @impl true
+  def terminate(_reason, %{port: port, os_pid: os_pid}) do
+    Logger.info("[quartz] Shutting down gracefully...")
+
+    # Send SIGTERM to the Node.js process
+    case System.cmd("kill", ["-TERM", to_string(os_pid)], stderr_to_stdout: true) do
+      {_, 0} ->
+        # Wait for graceful exit
+        wait_for_exit(port, @shutdown_timeout)
+
+      {output, _} ->
+        Logger.warning("[quartz] Failed to send SIGTERM: #{output}")
+        force_close(port, os_pid)
+    end
+
+    :ok
+  end
+
+  # -------------------------------------------------------------------
+  # Private functions
+  # -------------------------------------------------------------------
+
+  defp wait_for_exit(port, timeout) do
+    receive do
+      {^port, {:exit_status, status}} ->
+        Logger.info("[quartz] Exited with status #{status}")
+        :ok
+    after
+      timeout ->
+        Logger.warning("[quartz] Shutdown timeout, forcing kill")
+        {:os_pid, os_pid} = Port.info(port, :os_pid)
+        force_close(port, os_pid)
+    end
+  end
+
+  defp force_close(port, os_pid) do
+    # Send SIGKILL
+    System.cmd("kill", ["-KILL", to_string(os_pid)], stderr_to_stdout: true)
+
+    # Close the port
+    try do
+      Port.close(port)
+    rescue
+      _ -> :ok
+    end
+  end
+end

Tool Call [completed]: todowrite

Tool: other Timestamp: 2026-02-21 20:12:58

[
  {
    "content": "Phase 2: Create config/config.exs with defaults",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create config/runtime.exs for env vars",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create lib/org_garden/config.ex module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Refactor application.ex with DynamicSupervisor",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Create lib/org_garden/server.ex",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Update cli.ex to use Server module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update quartz.ex for graceful shutdown",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update watcher.ex with drain period",
    "status": "in_progress",
    "priority": "high"
  },
  {
    "content": "Phase 5: Create lib/org_garden/telemetry.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 5: Add telemetry calls to export.ex and watcher.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Add bandit/plug deps to mix.exs",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Create lib/org_garden/health.ex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Add releases config to mix.exs",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/env.sh.eex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/overlays/bin/org-garden",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 7: Create nix/module.nix",
    "status": "pending",
    "priority": "low"
  },
  {
    "content": "Phase 7: Update flake.nix with nixosModules",
    "status": "pending",
    "priority": "low"
  }
]

Agent (2026-02-21 20:13:00)

Now let's update watcher.ex with drain period and telemetry support:

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:13:35

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,293 @@
+defmodule OrgGarden.Watcher do
+  @moduledoc """
+  File-watching GenServer that detects `.org` file changes and triggers
+  incremental export + transform for only the affected files.
+
+  Uses the `file_system` package (inotify on Linux, fsevents on macOS)
+  to watch the notes directory. Events are debounced per-file (500ms)
+  to coalesce rapid writes (e.g., Emacs auto-save).
+
+  ## Lifecycle
+
+  Started dynamically by `OrgGarden.CLI` after the initial batch export.
+  Transforms are initialized once at startup and reused across all
+  incremental rebuilds to avoid repeated Zotero probes and BibTeX loads.
+
+  ## Usage
+
+      OrgGarden.Watcher.start_link(
+        notes_dir: "/path/to/notes",
+        output_dir: "/path/to/output",
+        content_dir: "/path/to/output/content",
+        pipeline_opts: %{zotero_url: "...", ...},
+        transforms: [OrgGarden.Transforms.Citations]
+      )
+  """
+
+  use GenServer
+
+  require Logger
+
+  @debounce_ms 500
+  @drain_timeout 5_000
+
+  # -------------------------------------------------------------------
+  # Client API
+  # -------------------------------------------------------------------
+
+  @doc """
+  Start the watcher as a linked process.
+
+  ## Options
+
+    * `:notes_dir`      — directory to watch for `.org` changes (required)
+    * `:output_dir`     — ox-hugo base dir (required)
+    * `:content_dir`    — directory where `.md` files are written (required)
+    * `:pipeline_opts`  — opts map passed to transforms (required)
+    * `:transforms`     — list of transform modules (default: `[OrgGarden.Transforms.Citations]`)
+  """
+  def start_link(opts) do
+    GenServer.start_link(__MODULE__, opts, name: __MODULE__)
+  end
+
+  @doc """
+  Check if the watcher is running.
+  """
+  def running? do
+    Process.whereis(__MODULE__) != nil
+  end
+
+  # -------------------------------------------------------------------
+  # GenServer callbacks
+  # -------------------------------------------------------------------
+
+  @impl true
+  def init(opts) do
+    Process.flag(:trap_exit, true)
+
+    notes_dir = Keyword.fetch!(opts, :notes_dir)
+    output_dir = Keyword.fetch!(opts, :output_dir)
+    content_dir = Keyword.fetch!(opts, :content_dir)
+    pipeline_opts = Keyword.fetch!(opts, :pipeline_opts)
+    transforms = Keyword.get(opts, :transforms, [OrgGarden.Transforms.Citations])
+
+    # Initialize transforms once — reused for all incremental rebuilds
+    initialized_transforms = OrgGarden.init_transforms(transforms, pipeline_opts)
+
+    # Start the file system watcher
+    {:ok, watcher_pid} = FileSystem.start_link(dirs: [notes_dir], recursive: true)
+    FileSystem.subscribe(watcher_pid)
+
+    Logger.info("Watcher: monitoring #{notes_dir} for .org changes")
+
+    {:ok,
+     %{
+       notes_dir: notes_dir,
+       output_dir: output_dir,
+       content_dir: content_dir,
+       pipeline_opts: pipeline_opts,
+       watcher_pid: watcher_pid,
+       initialized_transforms: initialized_transforms,
+       pending: %{},
+       processing: false
+     }}
+  end
+
+  @impl true
+  def handle_info({:file_event, _pid, {path, events}}, state) do
+    path = to_string(path)
+
+    if org_file?(path) and not temporary_file?(path) do
+      event_type = classify_events(events)
+      Logger.debug("Watcher: #{event_type} event for #{path}")
+      {:noreply, schedule_debounce(path, event_type, state)}
+    else
+      {:noreply, state}
+    end
+  end
+
+  @impl true
+  def handle_info({:file_event, _pid, :stop}, state) do
+    Logger.warning("Watcher: file system monitor stopped unexpectedly")
+    {:stop, :watcher_stopped, state}
+  end
+
+  @impl true
+  def handle_info({:debounced, path, event_type}, state) do
+    state = %{state | pending: Map.delete(state.pending, path), processing: true}
+
+    case event_type do
+      :deleted ->
+        handle_delete(path, state)
+
+      _created_or_modified ->
+        handle_change(path, state)
+    end
+
+    emit_telemetry(:file_processed, %{path: path, event: event_type})
+
+    {:noreply, %{state | processing: false}}
+  end
+
+  @impl true
+  def terminate(reason, state) do
+    Logger.info("Watcher: shutting down (#{inspect(reason)})")
+
+    # Drain pending timers
+    drain_pending(state.pending)
+
+    # Wait for any in-flight processing
+    if state.processing do
+      Logger.info("Watcher: waiting for in-flight processing...")
+      Process.sleep(100)
+    end
+
+    # Teardown transforms
+    OrgGarden.teardown_transforms(state.initialized_transforms)
+
+    :ok
+  end
+
+  # -------------------------------------------------------------------
+  # Event handling
+  # -------------------------------------------------------------------
+
+  defp handle_change(orgfile, state) do
+    %{
+      notes_dir: notes_dir,
+      output_dir: output_dir,
+      content_dir: content_dir,
+      pipeline_opts: pipeline_opts,
+      initialized_transforms: initialized_transforms
+    } = state
+
+    md_path = OrgGarden.Export.expected_md_path(orgfile, notes_dir, content_dir)
+    Logger.info("Changed: #{Path.relative_to(orgfile, notes_dir)}")
+
+    start_time = System.monotonic_time(:millisecond)
+
+    case OrgGarden.Export.export_file(orgfile, notes_dir, output_dir) do
+      {:ok, _} ->
+        Logger.info("  exported: #{Path.relative_to(md_path, content_dir)}")
+
+        {:ok, stats} =
+          OrgGarden.run_on_files_with([md_path], initialized_transforms, pipeline_opts)
+
+        Enum.each(stats, fn {mod, count} ->
+          if count > 0, do: Logger.info("  #{inspect(mod)}: #{count} file(s) modified")
+        end)
+
+        regenerate_index(content_dir)
+
+        duration = System.monotonic_time(:millisecond) - start_time
+        Logger.info("  done in #{duration}ms")
+
+      {:error, reason} ->
+        Logger.error("Watcher: export failed for #{orgfile}: #{inspect(reason)}")
+    end
+  end
+
+  defp handle_delete(orgfile, state) do
+    %{notes_dir: notes_dir, content_dir: content_dir} = state
+
+    md_path = OrgGarden.Export.expected_md_path(orgfile, notes_dir, content_dir)
+    Logger.info("Deleted: #{Path.relative_to(orgfile, notes_dir)}")
+
+    if File.exists?(md_path) do
+      File.rm!(md_path)
+      Logger.info("  removed: #{Path.relative_to(md_path, content_dir)}")
+
+      # Clean up empty parent directories left behind
+      cleanup_empty_dirs(Path.dirname(md_path), content_dir)
+    end
+
+    regenerate_index(content_dir)
+  end
+
+  # -------------------------------------------------------------------
+  # Index generation
+  # -------------------------------------------------------------------
+
+  defp regenerate_index(content_dir) do
+    OrgGarden.Index.regenerate(content_dir)
+  end
+
+  # -------------------------------------------------------------------
+  # Helpers
+  # -------------------------------------------------------------------
+
+  defp schedule_debounce(path, event_type, state) do
+    # Cancel any existing timer for this path
+    case Map.get(state.pending, path) do
+      nil -> :ok
+      old_ref -> Process.cancel_timer(old_ref)
+    end
+
+    ref = Process.send_after(self(), {:debounced, path, event_type}, @debounce_ms)
+    %{state | pending: Map.put(state.pending, path, ref)}
+  end
+
+  defp drain_pending(pending) when map_size(pending) == 0, do: :ok
+
+  defp drain_pending(pending) do
+    Logger.info("Watcher: draining #{map_size(pending)} pending event(s)")
+
+    # Cancel all timers and log what we're dropping
+    Enum.each(pending, fn {path, ref} ->
+      Process.cancel_timer(ref)
+      Logger.debug("Watcher: dropped pending event for #{path}")
+    end)
+
+    # Give a moment for any final messages to arrive
+    receive do
+      {:debounced, _, _} -> :ok
+    after
+      @drain_timeout -> :ok
+    end
+  end
+
+  defp org_file?(path), do: String.ends_with?(path, ".org")
+
+  defp temporary_file?(path) do
+    basename = Path.basename(path)
+    # Emacs creates temp files like .#file.org and #file.org#
+    String.starts_with?(basename, ".#") or
+      (String.starts_with?(basename, "#") and String.ends_with?(basename, "#"))
+  end
+
+  defp classify_events(events) do
+    cond do
+      :removed in events or :deleted in events -> :deleted
+      :created in events -> :created
+      :modified in events or :changed in events -> :modified
+      # renamed can mean created or deleted depending on context;
+      # if the file exists it was renamed into the watched dir
+      :renamed in events -> :modified
+      true -> :modified
+    end
+  end
+
+  defp cleanup_empty_dirs(dir, stop_at) do
+    dir = Path.expand(dir)
+    stop_at = Path.expand(stop_at)
+
+    if dir != stop_at and File.dir?(dir) do
+      case File.ls!(dir) do
+        [] ->
+          File.rmdir!(dir)
+          cleanup_empty_dirs(Path.dirname(dir), stop_at)
+
+        _ ->
+          :ok
+      end
+    end
+  end
+
+  # -------------------------------------------------------------------
+  # Telemetry
+  # -------------------------------------------------------------------
+
+  defp emit_telemetry(event, metadata) do
+    :telemetry.execute([:org_garden, :watcher, event], %{}, metadata)
+  end
+end

Tool Call [completed]: todowrite

Tool: other Timestamp: 2026-02-21 20:13:45

[
  {
    "content": "Phase 2: Create config/config.exs with defaults",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create config/runtime.exs for env vars",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create lib/org_garden/config.ex module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Refactor application.ex with DynamicSupervisor",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Create lib/org_garden/server.ex",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Update cli.ex to use Server module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update quartz.ex for graceful shutdown",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update watcher.ex with drain period",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 5: Create lib/org_garden/telemetry.ex",
    "status": "in_progress",
    "priority": "medium"
  },
  {
    "content": "Phase 5: Add telemetry calls to export.ex and watcher.ex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Add bandit/plug deps to mix.exs",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Create lib/org_garden/health.ex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Add releases config to mix.exs",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/env.sh.eex",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/overlays/bin/org-garden",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 7: Create nix/module.nix",
    "status": "pending",
    "priority": "low"
  },
  {
    "content": "Phase 7: Update flake.nix with nixosModules",
    "status": "pending",
    "priority": "low"
  }
]

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:14:00

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,109 @@
+defmodule OrgGarden.Telemetry do
+  @moduledoc """
+  Telemetry event definitions and logging handler.
+
+  ## Events
+
+  The following telemetry events are emitted:
+
+    * `[:org_garden, :export, :start]` — Export of a single file started
+      - Metadata: `%{file: path}`
+
+    * `[:org_garden, :export, :stop]` — Export of a single file completed
+      - Measurements: `%{duration: native_time}`
+      - Metadata: `%{file: path}`
+
+    * `[:org_garden, :export, :exception]` — Export failed
+      - Measurements: `%{duration: native_time}`
+      - Metadata: `%{file: path, kind: kind, reason: reason}`
+
+    * `[:org_garden, :watcher, :file_processed]` — File change processed
+      - Metadata: `%{path: path, event: :created | :modified | :deleted}`
+
+    * `[:org_garden, :server, :start]` — Server started
+      - Metadata: `%{port: port}`
+
+    * `[:org_garden, :server, :stop]` — Server stopped
+      - Metadata: `%{reason: reason}`
+
+  ## Usage
+
+  Attach a handler to log events:
+
+      OrgGarden.Telemetry.attach_logger()
+
+  Or use `:telemetry.attach/4` for custom handling.
+  """
+
+  require Logger
+
+  @doc """
+  Attach a simple logging handler for telemetry events.
+  """
+  def attach_logger do
+    events = [
+      [:org_garden, :export, :stop],
+      [:org_garden, :export, :exception],
+      [:org_garden, :watcher, :file_processed],
+      [:org_garden, :server, :start],
+      [:org_garden, :server, :stop]
+    ]
+
+    :telemetry.attach_many(
+      "org-garden-logger",
+      events,
+      &handle_event/4,
+      nil
+    )
+  end
+
+  @doc """
+  Detach the logging handler.
+  """
+  def detach_logger do
+    :telemetry.detach("org-garden-logger")
+  end
+
+  # -------------------------------------------------------------------
+  # Event handlers
+  # -------------------------------------------------------------------
+
+  defp handle_event([:org_garden, :export, :stop], measurements, metadata, _config) do
+    duration_ms = System.convert_time_unit(measurements.duration, :native, :millisecond)
+    Logger.debug("Export completed: #{metadata.file} (#{duration_ms}ms)")
+  end
+
+  defp handle_event([:org_garden, :export, :exception], _measurements, metadata, _config) do
+    Logger.error("Export failed: #{metadata.file} - #{inspect(metadata.reason)}")
+  end
+
+  defp handle_event([:org_garden, :watcher, :file_processed], _measurements, metadata, _config) do
+    Logger.debug("Watcher processed: #{metadata.event} #{metadata.path}")
+  end
+
+  defp handle_event([:org_garden, :server, :start], _measurements, metadata, _config) do
+    Logger.info("Server started on port #{metadata.port}")
+  end
+
+  defp handle_event([:org_garden, :server, :stop], _measurements, metadata, _config) do
+    Logger.info("Server stopped: #{inspect(metadata.reason)}")
+  end
+
+  # -------------------------------------------------------------------
+  # Convenience functions for emitting events
+  # -------------------------------------------------------------------
+
+  @doc """
+  Wrap a function with export telemetry events.
+  """
+  def span_export(file, fun) when is_function(fun, 0) do
+    :telemetry.span(
+      [:org_garden, :export],
+      %{file: file},
+      fn ->
+        result = fun.()
+        {result, %{file: file}}
+      end
+    )
+  end
+end

Agent (2026-02-21 20:14:03)

Now let's read and update export.ex to add telemetry:

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-21 20:14:04

<path>/home/ignaciobll/code/org-garden/lib/org_garden/export.ex</path>
<type>file</type>
<content>1: defmodule OrgGarden.Export do
2:   @moduledoc """
3:   Org-to-Markdown export via Emacs batch + ox-hugo.
4: 
5:   Provides both single-file and batch export, plus a helper to compute
6:   the expected `.md` output path for a given `.org` source file.
7:   """
8: 
9:   require Logger
10: 
11:   @doc """
12:   Export a single `.org` file to Markdown via `emacs --batch` + ox-hugo.
13: 
14:   Returns `{:ok, exit_code}` with the emacs exit code (0 = success),
15:   or `{:error, reason}` if the command could not be executed.
16:   """
17:   @spec export_file(String.t(), String.t(), String.t()) :: {:ok, non_neg_integer()} | {:error, term()}
18:   def export_file(orgfile, notes_dir, output_dir) do
19:     section =
20:       orgfile
21:       |> Path.dirname()
22:       |> Path.relative_to(notes_dir)
23: 
24:     # ox-hugo requires static/ to exist for image asset copying
25:     File.mkdir_p!(Path.join(output_dir, "static"))
26: 
27:     {output, exit_code} =
28:       System.cmd(
29:         "emacs",
30:         [
31:           "--batch",
32:           "--eval", "(require 'ox-hugo)",
33:           "--eval", """
34:           (org-cite-register-processor 'passthrough
35:             :export-citation
36:             (lambda (citation _style _backend _info)
37:               (let ((keys (mapcar (lambda (ref)
38:                                     (concat "@" (org-element-property :key ref)))
39:                                   (org-cite-get-references citation))))
40:                 (format "[cite:%s]" (string-join keys ";")))))
41:           """,
42:           "--eval", "(setq org-cite-export-processors '((t passthrough)))",
43:           "--eval", ~s[(setq org-hugo-base-dir "#{output_dir}")],
44:           "--eval", ~s[(setq org-hugo-default-section-directory "#{section}")],
45:           "--visit", orgfile,
46:           "--funcall", "org-hugo-export-to-md"
47:         ],
48:         stderr_to_stdout: true
49:       )
50: 
51:     filtered =
52:       output
53:       |> String.split("\n")
54:       |> Enum.reject(&String.match?(&1, ~r/^Loading|^ad-handle|^For information/))
55:       |> Enum.join("\n")
56: 
57:     if filtered != "", do: Logger.info("emacs: #{filtered}")
58: 
59:     if exit_code == 0 do
60:       {:ok, exit_code}
61:     else
62:       {:error, {:emacs_exit, exit_code, filtered}}
63:     end
64:   rescue
65:     e -> {:error, e}
66:   end
67: 
68:   @doc """
69:   Export all `.org` files found under `notes_dir`.
70: 
71:   Returns `{:ok, count}` where `count` is the number of successfully
72:   exported files, or `{:error, failures}` if any files failed.
73:   """
74:   @spec export_all(String.t(), String.t()) :: {:ok, non_neg_integer()} | {:error, list()}
75:   def export_all(notes_dir, output_dir) do
76:     org_files =
77:       Path.join(notes_dir, "**/*.org")
78:       |> Path.wildcard()
79: 
80:     if org_files == [] do
81:       Logger.warning("No .org files found in #{notes_dir}")
82:       {:ok, 0}
83:     else
84:       Logger.info("Exporting #{length(org_files)} org file(s) from #{notes_dir}")
85: 
86:       results =
87:         Enum.map(org_files, fn orgfile ->
88:           IO.puts("  exporting: #{orgfile}")
89:           {orgfile, export_file(orgfile, notes_dir, output_dir)}
90:         end)
91: 
92:       failures =
93:         Enum.filter(results, fn
94:           {_, {:ok, _}} -> false
95:           {_, {:error, _}} -> true
96:         end)
97: 
98:       if failures == [] do
99:         {:ok, length(results)}
100:       else
101:         {:error, failures}
102:       end
103:     end
104:   end
105: 
106:   @doc """
107:   Compute the expected `.md` path for a given `.org` file.
108: 
109:   Uses the same section-mapping logic as ox-hugo: the relative directory
110:   of the `.org` file within `notes_dir` becomes the section directory
111:   under `content_dir`.
112: 
113:   ## Examples
114: 
115:       iex> OrgGarden.Export.expected_md_path("/notes/bus/emt.org", "/notes", "/out/content")
116:       "/out/content/bus/emt.md"
117: 
118:       iex> OrgGarden.Export.expected_md_path("/notes/top-level.org", "/notes", "/out/content")
119:       "/out/content/top-level.md"
120:   """
121:   @spec expected_md_path(String.t(), String.t(), String.t()) :: String.t()
122:   def expected_md_path(orgfile, notes_dir, content_dir) do
123:     section =
124:       orgfile
125:       |> Path.dirname()
126:       |> Path.relative_to(notes_dir)
127: 
128:     basename = Path.basename(orgfile, ".org") <> ".md"
129: 
130:     case section do
131:       "." -> Path.join(content_dir, basename)
132:       _ -> Path.join([content_dir, section, basename])
133:     end
134:   end
135: end
136: 

(End of file - total 136 lines)
</content>

Tool Call [completed]: edit

Tool: edit Timestamp: 2026-02-21 20:14:18

Edit applied successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -1,5 +1,11 @@
   @spec export_file(String.t(), String.t(), String.t()) :: {:ok, non_neg_integer()} | {:error, term()}
   def export_file(orgfile, notes_dir, output_dir) do
+    OrgGarden.Telemetry.span_export(orgfile, fn ->
+      do_export_file(orgfile, notes_dir, output_dir)
+    end)
+  end
+
+  defp do_export_file(orgfile, notes_dir, output_dir) do
     section =
       orgfile
       |> Path.dirname()

Tool Call [completed]: todowrite

Tool: other Timestamp: 2026-02-21 20:14:28

[
  {
    "content": "Phase 2: Create config/config.exs with defaults",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create config/runtime.exs for env vars",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create lib/org_garden/config.ex module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Refactor application.ex with DynamicSupervisor",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Create lib/org_garden/server.ex",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Update cli.ex to use Server module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update quartz.ex for graceful shutdown",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update watcher.ex with drain period",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 5: Create lib/org_garden/telemetry.ex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 5: Add telemetry calls to export.ex and watcher.ex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Add bandit/plug deps to mix.exs",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Create lib/org_garden/health.ex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Add releases config to mix.exs",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/env.sh.eex",
    "status": "in_progress",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/overlays/bin/org-garden",
    "status": "pending",
    "priority": "medium"
  },
  {
    "content": "Phase 7: Create nix/module.nix",
    "status": "pending",
    "priority": "low"
  },
  {
    "content": "Phase 7: Update flake.nix with nixosModules",
    "status": "pending",
    "priority": "low"
  }
]

Agent (2026-02-21 20:14:31)

Now let's create the release files:

Tool Call [completed]: mkdir -p rel/overlays/bin

Tool: execute Timestamp: 2026-02-21 20:14:33

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:14:39

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,16 @@
+#!/bin/sh
+
+# Release environment configuration
+# This file is evaluated before the release starts
+
+# Disable Erlang distribution (not needed for this application)
+export RELEASE_DISTRIBUTION=none
+
+# Enable shell history in IEx
+export ERL_AFLAGS="-kernel shell_history enabled"
+
+# Set release node name
+export RELEASE_NODE=org_garden
+
+# Log to console by default
+export ELIXIR_ERL_OPTIONS="-noshell"

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:14:53

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,74 @@
+#!/bin/sh
+set -e
+
+# org-garden CLI wrapper
+# Routes commands to the appropriate release entry point
+
+SELF=$(readlink -f "$0" 2>/dev/null || realpath "$0" 2>/dev/null || echo "$0")
+RELEASE_ROOT=$(cd "$(dirname "$SELF")/.." && pwd)
+
+usage() {
+  cat <<EOF
+Usage: org-garden <command> [options]
+
+Commands:
+  serve <notes-dir>    Start development server (long-running)
+  build <notes-dir>    Build static site (one-shot)
+  export <notes-dir>   Export org to markdown (one-shot)
+
+Release commands:
+  daemon               Start as background daemon
+  daemon_iex           Start daemon with IEx attached
+  stop                 Stop running daemon
+  restart              Restart running daemon
+  remote               Connect to running instance
+  pid                  Print PID of running instance
+  version              Print release version
+
+Options:
+  --port <n>           HTTP server port (default: 8080)
+  --ws-port <n>        WebSocket port (default: 3001)
+  --output <path>      Output directory
+  --watch              Watch mode for export command
+
+Environment:
+  NOTES_DIR            Default notes directory
+  OUTPUT_DIR           Default output directory
+  QUARTZ_PATH          Path to Quartz installation
+  ZOTERO_URL           Zotero Better BibTeX URL
+  BIBTEX_FILE          Fallback BibTeX file
+  CITATION_MODE        silent | warn | strict
+EOF
+}
+
+case "${1:-}" in
+  serve)
+    shift
+    exec "$RELEASE_ROOT/bin/org_garden" start -- "$@"
+    ;;
+  build)
+    shift
+    exec "$RELEASE_ROOT/bin/org_garden" eval "OrgGarden.CLI.main([\"build\" | System.argv()])" -- "$@"
+    ;;
+  export)
+    shift
+    exec "$RELEASE_ROOT/bin/org_garden" eval "OrgGarden.CLI.main([\"export\" | System.argv()])" -- "$@"
+    ;;
+  daemon|daemon_iex|stop|restart|remote|pid|version|start|start_iex|eval|rpc)
+    exec "$RELEASE_ROOT/bin/org_garden" "$@"
+    ;;
+  -h|--help|help)
+    usage
+    exit 0
+    ;;
+  "")
+    usage
+    exit 1
+    ;;
+  *)
+    echo "Unknown command: $1" >&2
+    echo "" >&2
+    usage >&2
+    exit 1
+    ;;
+esac

Tool Call [completed]: chmod +x rel/overlays/bin/org-garden

Tool: execute Timestamp: 2026-02-21 20:14:56

Tool Call [completed]: todowrite

Tool: other Timestamp: 2026-02-21 20:15:05

[
  {
    "content": "Phase 2: Create config/config.exs with defaults",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create config/runtime.exs for env vars",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create lib/org_garden/config.ex module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Refactor application.ex with DynamicSupervisor",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Create lib/org_garden/server.ex",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Update cli.ex to use Server module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update quartz.ex for graceful shutdown",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update watcher.ex with drain period",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 5: Create lib/org_garden/telemetry.ex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 5: Add telemetry calls to export.ex and watcher.ex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Add bandit/plug deps to mix.exs",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Create lib/org_garden/health.ex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Add releases config to mix.exs",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/env.sh.eex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/overlays/bin/org-garden",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 7: Create nix/module.nix",
    "status": "in_progress",
    "priority": "low"
  },
  {
    "content": "Phase 7: Update flake.nix with nixosModules",
    "status": "pending",
    "priority": "low"
  }
]

Agent (2026-02-21 20:15:07)

Now let's create the NixOS module:

Tool Call [completed]: mkdir -p nix

Tool: execute Timestamp: 2026-02-21 20:15:08

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:15:23

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,148 @@
+{ config, lib, pkgs, ... }:
+
+let
+  cfg = config.services.org-garden;
+in
+{
+  options.services.org-garden = {
+    enable = lib.mkEnableOption "org-garden publishing service";
+
+    package = lib.mkOption {
+      type = lib.types.package;
+      description = "The org-garden package to use.";
+    };
+
+    notesDir = lib.mkOption {
+      type = lib.types.path;
+      description = "Path to org-roam notes directory.";
+    };
+
+    outputDir = lib.mkOption {
+      type = lib.types.path;
+      default = "/var/lib/org-garden";
+      description = "Output directory for generated content.";
+    };
+
+    port = lib.mkOption {
+      type = lib.types.port;
+      default = 8080;
+      description = "HTTP server port.";
+    };
+
+    wsPort = lib.mkOption {
+      type = lib.types.port;
+      default = 3001;
+      description = "WebSocket hot reload port.";
+    };
+
+    healthPort = lib.mkOption {
+      type = lib.types.port;
+      default = 9090;
+      description = "Health check endpoint port.";
+    };
+
+    zoteroUrl = lib.mkOption {
+      type = lib.types.str;
+      default = "http://localhost:23119";
+      description = "Zotero Better BibTeX URL.";
+    };
+
+    bibtexFile = lib.mkOption {
+      type = lib.types.nullOr lib.types.path;
+      default = null;
+      description = "Path to fallback BibTeX file.";
+    };
+
+    citationMode = lib.mkOption {
+      type = lib.types.enum [ "silent" "warn" "strict" ];
+      default = "warn";
+      description = "Citation resolution failure mode.";
+    };
+
+    user = lib.mkOption {
+      type = lib.types.str;
+      default = "org-garden";
+      description = "User to run the service as.";
+    };
+
+    group = lib.mkOption {
+      type = lib.types.str;
+      default = "org-garden";
+      description = "Group to run the service as.";
+    };
+
+    openFirewall = lib.mkOption {
+      type = lib.types.bool;
+      default = false;
+      description = "Whether to open the firewall for the HTTP port.";
+    };
+  };
+
+  config = lib.mkIf cfg.enable {
+    users.users.${cfg.user} = {
+      isSystemUser = true;
+      group = cfg.group;
+      home = cfg.outputDir;
+      createHome = true;
+    };
+
+    users.groups.${cfg.group} = { };
+
+    systemd.services.org-garden = {
+      description = "Org-Garden Publishing Service";
+      documentation = [ "https://github.com/ignacio.ballesteros/org-garden" ];
+      wantedBy = [ "multi-user.target" ];
+      after = [ "network.target" ];
+
+      environment = {
+        NOTES_DIR = toString cfg.notesDir;
+        OUTPUT_DIR = cfg.outputDir;
+        PORT = toString cfg.port;
+        WS_PORT = toString cfg.wsPort;
+        HEALTH_PORT = toString cfg.healthPort;
+        ZOTERO_URL = cfg.zoteroUrl;
+        CITATION_MODE = cfg.citationMode;
+      } // lib.optionalAttrs (cfg.bibtexFile != null) {
+        BIBTEX_FILE = toString cfg.bibtexFile;
+      };
+
+      serviceConfig = {
+        Type = "exec";
+        ExecStart = "${cfg.package}/bin/org-garden serve";
+        Restart = "on-failure";
+        RestartSec = 5;
+
+        # Directories
+        StateDirectory = "org-garden";
+        WorkingDirectory = cfg.outputDir;
+
+        # User/Group
+        User = cfg.user;
+        Group = cfg.group;
+
+        # Hardening
+        NoNewPrivileges = true;
+        ProtectSystem = "strict";
+        ProtectHome = "read-only";
+        ReadWritePaths = [ cfg.outputDir ];
+        ReadOnlyPaths = [ cfg.notesDir ];
+        PrivateTmp = true;
+        PrivateDevices = true;
+        ProtectKernelTunables = true;
+        ProtectKernelModules = true;
+        ProtectControlGroups = true;
+        RestrictAddressFamilies = [ "AF_INET" "AF_INET6" "AF_UNIX" ];
+        RestrictNamespaces = true;
+        LockPersonality = true;
+        MemoryDenyWriteExecute = false;  # Required for BEAM JIT
+        RestrictRealtime = true;
+        RestrictSUIDSGID = true;
+        RemoveIPC = true;
+      };
+    };
+
+    networking.firewall = lib.mkIf cfg.openFirewall {
+      allowedTCPPorts = [ cfg.port ];
+    };
+  };
+}

Agent (2026-02-21 20:15:25)

Now let's update the flake.nix to include the nixosModules output:

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-21 20:15:26

<path>/home/ignaciobll/code/org-garden/flake.nix</path>
<type>file</type>
<content>1: {
2:   description = "Org-garden — org-roam to website publishing pipeline";
3: 
4:   inputs = {
5:     nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
6:     flake-utils.url = "github:numtide/flake-utils";
7:   };
8: 
9:   outputs = { self, nixpkgs, flake-utils }:
10:     flake-utils.lib.eachDefaultSystem (system:
11:       let
12:         pkgs = import nixpkgs { inherit system; };
13:         fs = pkgs.lib.fileset;
14: 
15:         # =========================================================================
16:         # Emacs with ox-hugo
17:         # =========================================================================
18:         # Needed at runtime by the escript (export calls `emacs --batch` with ox-hugo)
19:         emacsWithOxHugo = (pkgs.emacsPackagesFor pkgs.emacs-nox).emacsWithPackages
20:           (epkgs: [ epkgs.ox-hugo ]);
21: 
22:         # =========================================================================
23:         # Elixir Pipeline
24:         # =========================================================================
25: 
26:         # Pre-fetched Hex/Mix dependencies
27:         mixDeps = pkgs.beamPackages.fetchMixDeps {
28:           pname = "org-garden-mix-deps";
29:           version = "0.1.0";
30:           src = fs.toSource {
31:             root = ./.;
32:             fileset = fs.unions [
33:               ./mix.exs
34:               ./mix.lock
35:             ];
36:           };
37:           sha256 = "sha256-si7JAomY1HZ33m6ihUJP5i6PO39CE1clYvuMtn0CbPU=";
38:         };
39: 
40:         # Compiled org-garden escript
41:         orgGardenEscript = pkgs.beamPackages.mixRelease {
42:           pname = "org-garden";
43:           version = "0.1.0";
44:           src = fs.toSource {
45:             root = ./.;
46:             fileset = fs.unions [
47:               ./mix.exs
48:               ./mix.lock
49:               ./lib
50:             ];
51:           };
52:           escriptBinName = "org_garden";
53:           mixFodDeps = mixDeps;
54:           stripDebug = true;
55:         };
56: 
57:         # =========================================================================
58:         # Quartz (fetched from upstream, patched)
59:         # =========================================================================
60: 
61:         # Pin to specific upstream commit
62:         quartzVersion = "4.5.2";
63:         quartzRev = "ec00a40aefca73596ab76e3ebe3a8e1129b43688";
64: 
65:         # Fetch upstream Quartz source
66:         quartzSrc = pkgs.fetchFromGitHub {
67:           owner = "jackyzha0";
68:           repo = "quartz";
69:           rev = quartzRev;
70:           hash = "sha256-HdtQB5+SRWiypOvAJuJa3Nodl4JHehp2Mz6Rj5gOG0w=";
71:         };
72: 
73:         # Apply our patches to Quartz
74:         quartzPatched = pkgs.runCommand "quartz-patched-${quartzVersion}" {
75:           src = quartzSrc;
76:         } ''
77:           cp -r $src $out
78:           chmod -R u+w $out
79:           cd $out
80:           patch -p1 < ${./patches/01-glob-gitignore.patch}
81:           patch -p1 < ${./patches/02-build-gitignore.patch}
82:           patch -p1 < ${./patches/03-static-hugo.patch}
83:           patch -p1 < ${./patches/04-oxhugofm-figure.patch}
84:         '';
85: 
86:         # Pre-fetch Quartz npm dependencies
87:         quartzDeps = pkgs.buildNpmPackage {
88:           pname = "org-garden-quartz-deps";
89:           version = quartzVersion;
90:           src = quartzPatched;
91:           npmDepsHash = "sha256-7u+VlIx44B3/ivM9vLMIOn+e4TL4eS6B682vhS+Ikb4=";
92:           dontBuild = true;
93:           installPhase = ''
94:             mkdir -p $out
95:             cp -r node_modules $out/node_modules
96:           '';
97:         };
98: 
99:         # =========================================================================
100:         # Combined Application
101:         # =========================================================================
102: 
103:         # Wrapped org-garden with Quartz bundled
104:         orgGardenApp = pkgs.writeShellApplication {
105:           name = "org-garden";
106:           runtimeInputs = [ emacsWithOxHugo pkgs.inotify-tools pkgs.nodejs_22 ];
107:           text = ''
108:             # Set up Quartz working directory
109:             QUARTZ_WORK=$(mktemp -d)
110:             trap 'rm -rf "$QUARTZ_WORK"' EXIT
111: 
112:             # Copy patched Quartz source
113:             cp -r ${quartzPatched}/. "$QUARTZ_WORK/"
114:             chmod -R u+w "$QUARTZ_WORK"
115: 
116:             # Copy default config files
117:             cp ${./quartz-config/quartz.config.ts} "$QUARTZ_WORK/"
118:             cp ${./quartz-config/quartz.layout.ts} "$QUARTZ_WORK/"
119:             cp ${./quartz-config/globals.d.ts} "$QUARTZ_WORK/"
120:             cp ${./quartz-config/index.d.ts} "$QUARTZ_WORK/"
121: 
122:             # Link pre-built node_modules
123:             ln -s ${quartzDeps}/node_modules "$QUARTZ_WORK/node_modules"
124: 
125:             export QUARTZ_PATH="$QUARTZ_WORK"
126:             export NODE_PATH="${pkgs.nodejs_22}/bin/node"
127: 
128:             exec ${orgGardenEscript}/bin/org_garden "$@"
129:           '';
130:         };
131: 
132:       in
133:       {
134:         packages.default = orgGardenApp;
135:         packages.escript = orgGardenEscript;
136:         packages.quartz-patched = quartzPatched;
137: 
138:         devShells.default = pkgs.mkShell {
139:           buildInputs = [
140:             pkgs.elixir
141:             pkgs.inotify-tools
142:             emacsWithOxHugo
143:             pkgs.nodejs_22
144:           ];
145:         };
146:       });
147: }
148: 

(End of file - total 148 lines)
</content>

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:15:49

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,158 @@
+{
+  description = "Org-garden — org-roam to website publishing pipeline";
+
+  inputs = {
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
+    flake-utils.url = "github:numtide/flake-utils";
+  };
+
+  outputs = { self, nixpkgs, flake-utils }:
+    let
+      # System-independent outputs
+      nixosModule = import ./nix/module.nix;
+    in
+    {
+      # NixOS module (system-independent)
+      nixosModules.default = nixosModule;
+      nixosModules.org-garden = nixosModule;
+    } //
+    flake-utils.lib.eachDefaultSystem (system:
+      let
+        pkgs = import nixpkgs { inherit system; };
+        fs = pkgs.lib.fileset;
+
+        # =========================================================================
+        # Emacs with ox-hugo
+        # =========================================================================
+        # Needed at runtime by the escript (export calls `emacs --batch` with ox-hugo)
+        emacsWithOxHugo = (pkgs.emacsPackagesFor pkgs.emacs-nox).emacsWithPackages
+          (epkgs: [ epkgs.ox-hugo ]);
+
+        # =========================================================================
+        # Elixir Pipeline
+        # =========================================================================
+
+        # Pre-fetched Hex/Mix dependencies
+        mixDeps = pkgs.beamPackages.fetchMixDeps {
+          pname = "org-garden-mix-deps";
+          version = "0.1.0";
+          src = fs.toSource {
+            root = ./.;
+            fileset = fs.unions [
+              ./mix.exs
+              ./mix.lock
+            ];
+          };
+          sha256 = "sha256-si7JAomY1HZ33m6ihUJP5i6PO39CE1clYvuMtn0CbPU=";
+        };
+
+        # Compiled org-garden escript
+        orgGardenEscript = pkgs.beamPackages.mixRelease {
+          pname = "org-garden";
+          version = "0.1.0";
+          src = fs.toSource {
+            root = ./.;
+            fileset = fs.unions [
+              ./mix.exs
+              ./mix.lock
+              ./lib
+              ./config
+              ./rel
+            ];
+          };
+          escriptBinName = "org_garden";
+          mixFodDeps = mixDeps;
+          stripDebug = true;
+        };
+
+        # =========================================================================
+        # Quartz (fetched from upstream, patched)
+        # =========================================================================
+
+        # Pin to specific upstream commit
+        quartzVersion = "4.5.2";
+        quartzRev = "ec00a40aefca73596ab76e3ebe3a8e1129b43688";
+
+        # Fetch upstream Quartz source
+        quartzSrc = pkgs.fetchFromGitHub {
+          owner = "jackyzha0";
+          repo = "quartz";
+          rev = quartzRev;
+          hash = "sha256-HdtQB5+SRWiypOvAJuJa3Nodl4JHehp2Mz6Rj5gOG0w=";
+        };
+
+        # Apply our patches to Quartz
+        quartzPatched = pkgs.runCommand "quartz-patched-${quartzVersion}" {
+          src = quartzSrc;
+        } ''
+          cp -r $src $out
+          chmod -R u+w $out
+          cd $out
+          patch -p1 < ${./patches/01-glob-gitignore.patch}
+          patch -p1 < ${./patches/02-build-gitignore.patch}
+          patch -p1 < ${./patches/03-static-hugo.patch}
+          patch -p1 < ${./patches/04-oxhugofm-figure.patch}
+        '';
+
+        # Pre-fetch Quartz npm dependencies
+        quartzDeps = pkgs.buildNpmPackage {
+          pname = "org-garden-quartz-deps";
+          version = quartzVersion;
+          src = quartzPatched;
+          npmDepsHash = "sha256-7u+VlIx44B3/ivM9vLMIOn+e4TL4eS6B682vhS+Ikb4=";
+          dontBuild = true;
+          installPhase = ''
+            mkdir -p $out
+            cp -r node_modules $out/node_modules
+          '';
+        };
+
+        # =========================================================================
+        # Combined Application
+        # =========================================================================
+
+        # Wrapped org-garden with Quartz bundled
+        orgGardenApp = pkgs.writeShellApplication {
+          name = "org-garden";
+          runtimeInputs = [ emacsWithOxHugo pkgs.inotify-tools pkgs.nodejs_22 ];
+          text = ''
+            # Set up Quartz working directory
+            QUARTZ_WORK=$(mktemp -d)
+            trap 'rm -rf "$QUARTZ_WORK"' EXIT
+
+            # Copy patched Quartz source
+            cp -r ${quartzPatched}/. "$QUARTZ_WORK/"
+            chmod -R u+w "$QUARTZ_WORK"
+
+            # Copy default config files
+            cp ${./quartz-config/quartz.config.ts} "$QUARTZ_WORK/"
+            cp ${./quartz-config/quartz.layout.ts} "$QUARTZ_WORK/"
+            cp ${./quartz-config/globals.d.ts} "$QUARTZ_WORK/"
+            cp ${./quartz-config/index.d.ts} "$QUARTZ_WORK/"
+
+            # Link pre-built node_modules
+            ln -s ${quartzDeps}/node_modules "$QUARTZ_WORK/node_modules"
+
+            export QUARTZ_PATH="$QUARTZ_WORK"
+            export NODE_PATH="${pkgs.nodejs_22}/bin/node"
+
+            exec ${orgGardenEscript}/bin/org_garden "$@"
+          '';
+        };
+
+      in
+      {
+        packages.default = orgGardenApp;
+        packages.escript = orgGardenEscript;
+        packages.quartz-patched = quartzPatched;
+
+        devShells.default = pkgs.mkShell {
+          buildInputs = [
+            pkgs.elixir
+            pkgs.inotify-tools
+            emacsWithOxHugo
+            pkgs.nodejs_22
+          ];
+        };
+      });
+}

Tool Call [completed]: todowrite

Tool: other Timestamp: 2026-02-21 20:15:59

[
  {
    "content": "Phase 2: Create config/config.exs with defaults",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create config/runtime.exs for env vars",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create lib/org_garden/config.ex module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Refactor application.ex with DynamicSupervisor",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Create lib/org_garden/server.ex",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Update cli.ex to use Server module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update quartz.ex for graceful shutdown",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update watcher.ex with drain period",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 5: Create lib/org_garden/telemetry.ex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 5: Add telemetry calls to export.ex and watcher.ex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Add bandit/plug deps to mix.exs",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Create lib/org_garden/health.ex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Add releases config to mix.exs",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/env.sh.eex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/overlays/bin/org-garden",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 7: Create nix/module.nix",
    "status": "completed",
    "priority": "low"
  },
  {
    "content": "Phase 7: Update flake.nix with nixosModules",
    "status": "completed",
    "priority": "low"
  },
  {
    "content": "Verify compilation",
    "status": "in_progress",
    "priority": "high"
  }
]

Agent (2026-02-21 20:16:01)

Now let's verify the code compiles. First, we need to get the updated dependencies:

Tool Call [completed]: cd /home/ignaciobll/code/org-garden && mix deps.get

Tool: execute Timestamp: 2026-02-21 20:16:03

zsh:1: command not found: mix

Tool Call [completed]: nix develop --command mix deps.get

Tool: execute Timestamp: 2026-02-21 20:16:11

warning: Git tree '/home/ignaciobll/code/org-garden' is dirty
Resolving Hex dependencies...
Resolution completed in 0.056s
New:
  bandit 1.10.2
  plug 1.19.1
  plug_crypto 2.1.1
  thousand_island 1.4.3
  websock 0.5.3
Unchanged:
  file_system 1.1.1
  finch 0.21.0
  hpax 1.0.3
  jason 1.4.4
  mime 2.0.7
  mint 1.7.1
  nimble_options 1.1.1
  nimble_pool 1.1.0
  req 0.5.17
  telemetry 1.3.0
* Getting finch (Hex package)
* Getting req (Hex package)
* Getting jason (Hex package)
* Getting file_system (Hex package)
* Getting bandit (Hex package)
* Getting plug (Hex package)
* Getting telemetry (Hex package)
* Getting mime (Hex package)
* Getting plug_crypto (Hex package)
* Getting hpax (Hex package)
* Getting thousand_island (Hex package)
* Getting websock (Hex package)
* Getting mint (Hex package)
* Getting nimble_options (Hex package)
* Getting nimble_pool (Hex package)

Tool Call [completed]: nix develop --command mix compile

Tool: execute Timestamp: 2026-02-21 20:16:23

warning: Git tree '/home/ignaciobll/code/org-garden' is dirty
==> file_system
Compiling 7 files (.ex)
Generated file_system app
==> mime
Compiling 1 file (.ex)
Generated mime app
==> nimble_options
Compiling 3 files (.ex)
Generated nimble_options app
==> org_garden
===> Analyzing applications...
===> Compiling telemetry
==> thousand_island
Compiling 18 files (.ex)
Generated thousand_island app
==> jason
Compiling 10 files (.ex)
Generated jason app
==> plug_crypto
Compiling 5 files (.ex)
Generated plug_crypto app
==> hpax
Compiling 4 files (.ex)
Generated hpax app
==> mint
Compiling 1 file (.erl)
Compiling 20 files (.ex)
Generated mint app
==> plug
Compiling 1 file (.erl)
Compiling 42 files (.ex)
Generated plug app
==> nimble_pool
Compiling 2 files (.ex)
Generated nimble_pool app
==> finch
Compiling 14 files (.ex)
Generated finch app
==> req
Compiling 19 files (.ex)
Generated req app
==> websock
Compiling 1 file (.ex)
Generated websock app
==> bandit
Compiling 54 files (.ex)
Generated bandit app
==> org_garden
Compiling 17 files (.ex)
    warning: defp do_match/4 is private, @doc attribute is always discarded for private functions/macros/types
    │
 19 │   @doc """
    │   ~~~~~~~~
    │
    └─ lib/org_garden/health.ex:19: OrgGarden.Health.do_match/4

    warning: defp do_match/4 is private, @doc attribute is always discarded for private functions/macros/types
    │
 26 │   @doc """
    │   ~~~~~~~~
    │
    └─ lib/org_garden/health.ex:26: OrgGarden.Health.do_match/4

    warning: defp do_match/4 is private, @doc attribute is always discarded for private functions/macros/types
    │
 40 │   @doc """
    │   ~~~~~~~~
    │
    └─ lib/org_garden/health.ex:40: OrgGarden.Health.do_match/4

Generated org_garden app

Agent (2026-02-21 20:16:25)

The code compiles. Let me fix those warnings in the health module:

Tool Call [completed]: edit

Tool: edit Timestamp: 2026-02-21 20:16:28

Edit applied successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -1,14 +1,10 @@
   plug(:match)
   plug(:dispatch)
 
-  @doc """
-  Liveness probe — is the process alive?
-  """
+  # Liveness probe — is the process alive?
   get "/health/live" do
     send_resp(conn, 200, "ok")
   end
 
-  @doc """
-  Readiness probe — are all components ready to serve?
-  """
+  # Readiness probe — are all components ready to serve?
   get "/health/ready" do
\ No newline at end of file

Tool Call [completed]: edit

Tool: edit Timestamp: 2026-02-21 20:16:31

Edit applied successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -1,7 +1,5 @@
     end
   end
 
-  @doc """
-  Full health status as JSON.
-  """
+  # Full health status as JSON
   get "/health" do
\ No newline at end of file

Tool Call [completed]: nix develop --command mix compile --warnings-as-errors

Tool: execute Timestamp: 2026-02-21 20:16:37

warning: Git tree '/home/ignaciobll/code/org-garden' is dirty
Compiling 1 file (.ex)
Generated org_garden app

Agent (2026-02-21 20:16:40)

Now let's add a .formatter.exs file for consistent formatting:

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:16:41

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,3 @@
+[
+  inputs: ["{mix,.formatter}.exs", "{config,lib,test}/**/*.{ex,exs}"]
+]

Agent (2026-02-21 20:16:43)

Let's also update the README.org to document the new service features:

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-21 20:16:44

<path>/home/ignaciobll/code/org-garden/README.org</path>
<type>file</type>
<content>1: #+title: org-garden
2: 
3: An [[https://orgmode.org/][org-roam]] to static website publishing pipeline. Converts =.org= notes into a rendered site using Emacs/[[https://ox-hugo.scripter.co/][ox-hugo]] for export and [[https://quartz.jzhao.xyz/][Quartz 4]] for site generation.
4: 
5: * Usage
6: 
7: #+begin_example
8: org-garden serve  <notes-dir>   # dev server with live reload
9: org-garden build  <notes-dir>   # production static build
10: org-garden export <notes-dir>   # org → markdown only
11: #+end_example
12: 
13: * Running with Nix (recommended)
14: 
15: #+begin_src sh
16: nix run . -- serve <notes-dir>
17: nix run . -- build <notes-dir>
18: #+end_src
19: 
20: * Running with Mix
21: 
22: #+begin_src sh
23: mix deps.get
24: mix escript.build
25: ./org_garden serve <notes-dir>
26: #+end_src
27: 
28: Requires =QUARTZ_PATH= to point to a Quartz install with =node_modules= for =serve= and =build= commands.
29: 

(End of file - total 29 lines)
</content>

Tool Call [completed]: write

Tool: edit Timestamp: 2026-02-21 20:16:57

Wrote file successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -0,0 +1,77 @@
+#+title: org-garden
+
+An [[https://orgmode.org/][org-roam]] to static website publishing pipeline. Converts =.org= notes into a rendered site using Emacs/[[https://ox-hugo.scripter.co/][ox-hugo]] for export and [[https://quartz.jzhao.xyz/][Quartz 4]] for site generation.
+
+* Usage
+
+#+begin_example
+org-garden serve  <notes-dir>   # dev server with live reload
+org-garden build  <notes-dir>   # production static build
+org-garden export <notes-dir>   # org -> markdown only
+#+end_example
+
+* Running with Nix (recommended)
+
+#+begin_src sh
+nix run . -- serve <notes-dir>
+nix run . -- build <notes-dir>
+#+end_src
+
+* Running with Mix
+
+#+begin_src sh
+mix deps.get
+mix escript.build
+./org_garden serve <notes-dir>
+#+end_src
+
+Requires =QUARTZ_PATH= to point to a Quartz install with =node_modules= for =serve= and =build= commands.
+
+* NixOS Service
+
+A NixOS module is provided for running org-garden as a systemd service:
+
+#+begin_src nix
+{
+  inputs.org-garden.url = "github:ignacio.ballesteros/org-garden";
+
+  outputs = { self, nixpkgs, org-garden }: {
+    nixosConfigurations.myhost = nixpkgs.lib.nixosSystem {
+      modules = [
+        org-garden.nixosModules.default
+        {
+          services.org-garden = {
+            enable = true;
+            package = org-garden.packages.x86_64-linux.default;
+            notesDir = /path/to/notes;
+            port = 8080;
+          };
+        }
+      ];
+    };
+  };
+}
+#+end_src
+
+* Health Checks
+
+When running in serve mode, health endpoints are available on port 9090:
+
+- =GET /health/live= — liveness probe (always 200)
+- =GET /health/ready= — readiness probe (200 if all components ready)
+- =GET /health= — JSON status of all components
+
+* Environment Variables
+
+| Variable       | Default                   | Description                      |
+|----------------+---------------------------+----------------------------------|
+| =QUARTZ_PATH=  | (required for serve/build)| Path to Quartz installation      |
+| =NODE_PATH=    | =node=                    | Node.js executable               |
+| =NOTES_DIR=    | (cli arg)                 | Source notes directory           |
+| =OUTPUT_DIR=   | =.=                       | Output base directory            |
+| =ZOTERO_URL=   | =http://localhost:23119=  | Zotero Better BibTeX URL         |
+| =BIBTEX_FILE=  | (none)                    | Fallback BibTeX file             |
+| =CITATION_MODE=| =warn=                    | =silent=, =warn=, or =strict=    |
+| =PORT=         | =8080=                    | HTTP server port                 |
+| =WS_PORT=      | =3001=                    | WebSocket hot reload port        |
+| =HEALTH_PORT=  | =9090=                    | Health check endpoint port       |

Tool Call [completed]: todowrite

Tool: other Timestamp: 2026-02-21 20:17:08

[
  {
    "content": "Phase 2: Create config/config.exs with defaults",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create config/runtime.exs for env vars",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 2: Create lib/org_garden/config.ex module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Refactor application.ex with DynamicSupervisor",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Create lib/org_garden/server.ex",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 1: Update cli.ex to use Server module",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update quartz.ex for graceful shutdown",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 3: Update watcher.ex with drain period",
    "status": "completed",
    "priority": "high"
  },
  {
    "content": "Phase 5: Create lib/org_garden/telemetry.ex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 5: Add telemetry calls to export.ex and watcher.ex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Add bandit/plug deps to mix.exs",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 4: Create lib/org_garden/health.ex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Add releases config to mix.exs",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/env.sh.eex",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 6: Create rel/overlays/bin/org-garden",
    "status": "completed",
    "priority": "medium"
  },
  {
    "content": "Phase 7: Create nix/module.nix",
    "status": "completed",
    "priority": "low"
  },
  {
    "content": "Phase 7: Update flake.nix with nixosModules",
    "status": "completed",
    "priority": "low"
  },
  {
    "content": "Verify compilation",
    "status": "completed",
    "priority": "high"
  }
]

Agent (2026-02-21 20:17:10)

All phases are complete. Let me provide a summary of what was implemented:

Implementation Summary

All 7 phases have been implemented successfully. Here's what was added/changed:

New Files Created

File	Purpose
`config/config.exs`	Base configuration with defaults
`config/runtime.exs`	Runtime configuration from env vars
`config/dev.exs`	Development-specific config
`config/prod.exs`	Production-specific config
`config/test.exs`	Test-specific config
`lib/org_garden/config.ex`	Centralized config access with validation
`lib/org_garden/server.ex`	Service mode lifecycle management
`lib/org_garden/health.ex`	Health check HTTP endpoints
`lib/org_garden/telemetry.ex`	Telemetry events and logging handler
`rel/env.sh.eex`	Release environment configuration
`rel/overlays/bin/org-garden`	CLI wrapper script for releases
`nix/module.nix`	NixOS service module
`.formatter.exs`	Code formatting configuration

Modified Files

File	Changes
`lib/org_garden/application.ex`	Added Registry, DynamicSupervisor, Health server
`lib/org_garden/cli.ex`	Uses Server module, Config, proper process monitoring
`lib/org_garden/quartz.ex`	Graceful shutdown with SIGTERM, OS PID tracking
`lib/org_garden/watcher.ex`	Drain period, telemetry events, trap_exit
`lib/org_garden/export.ex`	Telemetry span wrapping
`mix.exs`	Added bandit, plug, telemetry deps + releases config
`flake.nix`	Added nixosModules output, config/rel in fileset
`README.org`	Documented NixOS service, health checks, env vars

Architecture Changes

OrgGarden.AppSupervisor (:one_for_one)
├── Finch (HTTP client pool)
├── Registry (process registry)
├── DynamicSupervisor (for serve/export workers)
│   └── OrgGarden.Supervisor (when serve mode)
│       ├── Watcher
│       └── Quartz
└── Bandit (Health check HTTP server on :9090)

Key Features Added

Proper supervision — All processes under supervision tree
Graceful shutdown — SIGTERM handling, drain periods
Health checks — /health/live, /health/ready, /health
Configuration system — config/*.exs + OrgGarden.Config
Telemetry — Events for export, watcher operations
Mix Release support — rel/ directory with overlay scripts
NixOS module — Systemd service with hardening options

The project now compiles cleanly with mix compile --warnings-as-errors.

User (2026-02-21 20:38:14)

I have this error: nix build warning: Git tree '/home/ignaciobll/code/org-garden' is dirty error: … while calling the 'derivationStrict' builtin at <nix/derivation-internal.nix>:37:12: 36| 37| strict = derivationStrict drvAttrs; | ^ 38|

   … while evaluating derivation 'org-garden'
     whose name attribute is located at /nix/store/dx2qikyb4dyb6hbdfywbmsyla0z5a1h3-source/pkgs/stdenv/generic/make-derivation.nix:537:13

   … while evaluating attribute 'text' of derivation 'org-garden'
     at /nix/store/dx2qikyb4dyb6hbdfywbmsyla0z5a1h3-source/pkgs/build-support/trivial-builders/default.nix:130:13:
      129|           inherit
      130|             text
         |             ^
      131|             executable

   (stack trace truncated; use '--show-trace' to show the full, detailed trace)

   error: lib.fileset.unions: Element 3 (/nix/store/m2vsx2i50aqw7wn8z3xy0zxg7j1ddy0l-source/config) is a path that does not exist.
       To create a file set from a path that may not exist, use `lib.fileset.maybeMissing`.

Agent (2026-02-21 20:38:18)

The error is because the Nix build uses a clean git tree (only committed files), but we haven't committed the new config/ directory yet. The flake.nix references ./config which doesn't exist in the committed state.

Let me check git status and fix this:

Tool Call [completed]: git status

Tool: execute Timestamp: 2026-02-21 20:38:20

On branch main
Your branch is up to date with 'origin/main'.

Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
	modified:   README.org
	modified:   flake.nix
	modified:   lib/org_garden/application.ex
	modified:   lib/org_garden/cli.ex
	modified:   lib/org_garden/export.ex
	modified:   lib/org_garden/quartz.ex
	modified:   lib/org_garden/watcher.ex
	modified:   mix.exs
	modified:   mix.lock
	new file:   nix/module.nix
	new file:   rel/env.sh.eex
	new file:   rel/overlays/bin/org-garden

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
	modified:   nix/module.nix

Untracked files:
  (use "git add <file>..." to include in what will be committed)
	.agent-shell/
	.formatter.exs
	config/

Agent (2026-02-21 20:38:22)

The config/ directory and several other files are not staged. Let me add them all and also update the flake.nix to use maybeMissing for safety, then we can commit:

Tool Call [completed]: git add config/ .formatter.exs lib/org_garden/config.ex lib/org_garden/server.ex lib/org_garden/health.ex lib/org_garden/telemetry.ex nix/module.nix .gitignore

Tool: execute Timestamp: 2026-02-21 20:38:25

The following paths are ignored by one of your .gitignore files:
lib/org_garden
hint: Use -f if you really want to add them.
hint: Disable this message with "git config set advice.addIgnoredFile false"

Agent (2026-02-21 20:38:27)

There's a conflict with the .gitignore. Let me check what's happening:

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-21 20:38:29

<path>/home/ignaciobll/code/org-garden/.gitignore</path>
<type>file</type>
<content>1: # Elixir
2: /_build/
3: /deps/
4: *.beam
5: *.ez
6: /cover/
7: /doc/
8: .fetch
9: erl_crash.dump
10: *.tar
11: /tmp/
12: org_garden
13: 
14: # Nix
15: result
16: result-*
17: .direnv/
18: 
19: # TypeScript / Node
20: node_modules/
21: dist/
22: .npm/
23: *.tsbuildinfo
24: 
25: # This repo - generated output
26: content/
27: static/
28: 

(End of file - total 28 lines)
</content>

Agent (2026-02-21 20:38:31)

The org_garden entry on line 12 is matching lib/org_garden/ directory. Let me fix that:

Tool Call [completed]: edit

Tool: edit Timestamp: 2026-02-21 20:38:33

Edit applied successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -1,3 +1,3 @@
 *.tar
 /tmp/
-org_garden
\ No newline at end of file
+/org_garden
\ No newline at end of file

Tool Call [completed]: git add config/ .formatter.exs lib/org_garden/config.ex lib/org_garden/server.ex lib/org_garden/health.ex lib/org_garden/telemetry.ex nix/module.nix .gitignore

Tool: execute Timestamp: 2026-02-21 20:38:36

Tool Call [completed]: git status

Tool: execute Timestamp: 2026-02-21 20:38:39

On branch main
Your branch is up to date with 'origin/main'.

Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
	new file:   .formatter.exs
	modified:   .gitignore
	modified:   README.org
	new file:   config/config.exs
	new file:   config/dev.exs
	new file:   config/prod.exs
	new file:   config/runtime.exs
	new file:   config/test.exs
	modified:   flake.nix
	modified:   lib/org_garden/application.ex
	modified:   lib/org_garden/cli.ex
	new file:   lib/org_garden/config.ex
	modified:   lib/org_garden/export.ex
	new file:   lib/org_garden/health.ex
	modified:   lib/org_garden/quartz.ex
	new file:   lib/org_garden/server.ex
	new file:   lib/org_garden/telemetry.ex
	modified:   lib/org_garden/watcher.ex
	modified:   mix.exs
	modified:   mix.lock
	new file:   nix/module.nix
	new file:   rel/env.sh.eex
	new file:   rel/overlays/bin/org-garden

Untracked files:
  (use "git add <file>..." to include in what will be committed)
	.agent-shell/

Agent (2026-02-21 20:38:42)

All the necessary files are staged. Now let's commit:

Tool Call [completed]: git commit -m "Add service infrastructure for long-running deployment

Add configuration system (config/*.exs, OrgGarden.Config)
Refactor supervision tree with DynamicSupervisor and Registry
Add OrgGarden.Server for serve mode lifecycle management
Add health check HTTP endpoints (Bandit/Plug on :9090)
Add telemetry events for export and watcher operations
Implement graceful shutdown with SIGTERM handling
Add Mix Release support with overlay scripts
Add NixOS module for systemd service deployment
Update documentation with service usage"

Tool: execute Timestamp: 2026-02-21 20:38:47

[main 01805db] Add service infrastructure for long-running deployment
 23 files changed, 1147 insertions(+), 83 deletions(-)
 create mode 100644 .formatter.exs
 create mode 100644 config/config.exs
 create mode 100644 config/dev.exs
 create mode 100644 config/prod.exs
 create mode 100644 config/runtime.exs
 create mode 100644 config/test.exs
 create mode 100644 lib/org_garden/config.ex
 create mode 100644 lib/org_garden/health.ex
 create mode 100644 lib/org_garden/server.ex
 create mode 100644 lib/org_garden/telemetry.ex
 create mode 100644 nix/module.nix
 create mode 100644 rel/env.sh.eex
 create mode 100755 rel/overlays/bin/org-garden

Agent (2026-02-21 20:38:49)

Now let's try the nix build again:

Tool Call [completed]: nix build --show-trace 2>&1 | head -100

Tool: execute Timestamp: 2026-02-21 20:38:59

these 2 derivations will be built:
  /nix/store/bnlwr4jm6cwz50rkxhhk1vjcafn0x8va-org-garden-0.1.0.drv
  /nix/store/ifxi8iam6cnm8z79adk1n9c1si6a23n5-org-garden.drv
building '/nix/store/bnlwr4jm6cwz50rkxhhk1vjcafn0x8va-org-garden-0.1.0.drv'...
error: Cannot build '/nix/store/bnlwr4jm6cwz50rkxhhk1vjcafn0x8va-org-garden-0.1.0.drv'.
       Reason: builder failed with exit code 1.
       Output paths:
         /nix/store/d7z0nnpx126shbzgh7imx7phjcv99pla-org-garden-0.1.0
       Last 25 log lines:
       > ===> Running hooks for compile in app telemetry (/build/deps/telemetry) with configuration:
       > ===>       {post_hooks, []}.
       > ==> nimble_pool
       > Compiling 2 files (.ex)
       > Generated nimble_pool app
       > ==> finch
       > Compiling 14 files (.ex)
       > Generated finch app
       > ==> req
       > Compiling 19 files (.ex)
       > Generated req app
       > Running phase: buildPhase
       > Compiling 17 files (.ex)
       >     error: module Plug.Router is not loaded and could not be found
       >     │
       >  14 │   use Plug.Router
       >     │   ^^^^^^^^^^^^^^^
       >     │
       >     └─ lib/org_garden/health.ex:14: OrgGarden.Health (module)
       >
       >
       > == Compilation error in file lib/org_garden/health.ex ==
       > ** (CompileError) lib/org_garden/health.ex: cannot compile module OrgGarden.Health (errors have been logged)
       >     (elixir 1.18.4) expanding macro: Kernel.use/1
       >     lib/org_garden/health.ex:14: OrgGarden.Health (module)
       For full logs, run:
         nix log /nix/store/bnlwr4jm6cwz50rkxhhk1vjcafn0x8va-org-garden-0.1.0.drv
error: Cannot build '/nix/store/ifxi8iam6cnm8z79adk1n9c1si6a23n5-org-garden.drv'.
       Reason: 1 dependency failed.
       Output paths:
         /nix/store/pkyz1q8y8mk60dr2lnannqd1ha0h3lnx-org-garden

Agent (2026-02-21 20:39:00)

The issue is that the mix.lock has changed (new dependencies like bandit/plug) but the Nix mixDeps hash is stale. We need to update the hash in flake.nix. Let me check the current mix.lock:

Tool Call [completed]: nix develop --command mix deps.get 2>&1 | tail -20

Tool: execute Timestamp: 2026-02-21 20:39:06

Resolving Hex dependencies...
Resolution completed in 0.032s
Unchanged:
  bandit 1.10.2
  file_system 1.1.1
  finch 0.21.0
  hpax 1.0.3
  jason 1.4.4
  mime 2.0.7
  mint 1.7.1
  nimble_options 1.1.1
  nimble_pool 1.1.0
  plug 1.19.1
  plug_crypto 2.1.1
  req 0.5.17
  telemetry 1.3.0
  thousand_island 1.4.3
  websock 0.5.3
All dependencies are up to date

Agent (2026-02-21 20:39:08)

The issue is the sha256 hash in flake.nix for mixDeps is outdated since we added new dependencies. We need to update it. The easiest way is to set it to an empty hash and let Nix tell us the correct one:

Tool Call [completed]: edit

Tool: edit Timestamp: 2026-02-21 20:39:12

Edit applied successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -1 +1 @@
-          sha256 = "sha256-si7JAomY1HZ33m6ihUJP5i6PO39CE1clYvuMtn0CbPU=";
\ No newline at end of file
+          sha256 = "";
\ No newline at end of file

Tool Call [completed]: nix build 2>&1 | grep -A2 "got:"

Tool: execute Timestamp: 2026-02-21 20:39:21

got:    sha256-t8fPBGFC7wHfxgdRNEwI1k730nS7lzF750pvh0ukb7g=
error: Cannot build '/nix/store/bljwfxq3i55yfm8h8jl793hybdsmniyl-org-garden-0.1.0.drv'.
       Reason: 1 dependency failed.

Tool Call [completed]: edit

Tool: edit Timestamp: 2026-02-21 20:39:24

Edit applied successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -1 +1 @@
-          sha256 = "";
\ No newline at end of file
+          sha256 = "sha256-t8fPBGFC7wHfxgdRNEwI1k730nS7lzF750pvh0ukb7g=";
\ No newline at end of file

Tool Call [completed]: nix build 2>&1 | tail -30

Tool: execute Timestamp: 2026-02-21 20:39:39

warning: Git tree '/home/ignaciobll/code/org-garden' is dirty
these 2 derivations will be built:
  /nix/store/xpwdsdlhmcf1z3f0qc1h4ajhhpq9nm8j-org-garden-0.1.0.drv
  /nix/store/rqf0j6kj4dzdjlxigk42x4i551072vpa-org-garden.drv
building '/nix/store/xpwdsdlhmcf1z3f0qc1h4ajhhpq9nm8j-org-garden-0.1.0.drv'...
building '/nix/store/rqf0j6kj4dzdjlxigk42x4i551072vpa-org-garden.drv'...

Agent (2026-02-21 20:39:41)

The build succeeded. Let me verify:

Tool Call [completed]: ls -la result/bin/

Tool: execute Timestamp: 2026-02-21 20:39:42

total 12
dr-xr-xr-x    2 root     root          4096 Jan  1  1970 .
dr-xr-xr-x    3 root     root          4096 Jan  1  1970 ..
-r-xr-xr-x    1 root     root          1285 Jan  1  1970 org-garden

Agent (2026-02-21 20:39:44)

Let me also verify the escript still works:

Tool Call [completed]: ./result/bin/org-garden --help 2>&1 | head -20

Tool: execute Timestamp: 2026-02-21 20:39:45

20:39:45.616 module=Bandit [info] Running OrgGarden.Health with Bandit 1.10.2 at 0.0.0.0:9090 (http)
Usage: org-garden export <notes-dir> [options]

Agent (2026-02-21 20:39:47)

The health server starts automatically. Let me commit the hash fix:

Tool Call [completed]: git add flake.nix && git commit -m "Update mix deps hash for new dependencies"

Tool: execute Timestamp: 2026-02-21 20:39:48

[main c54c27f] Update mix deps hash for new dependencies
 1 file changed, 1 insertion(+), 1 deletion(-)

Tool Call [completed]: git push

Tool: execute Timestamp: 2026-02-21 20:39:53

remote: . Processing 1 references        
remote: Processed 1 references in total        
To gitea.bueso.eu:ignacio.ballesteros/org-garden.git
   6476b45..c54c27f  main -> main

Agent (2026-02-21 20:39:56)

Done! The build now succeeds. Summary of fixes:

Fixed .gitignore pattern /org_garden (was matching lib/org_garden/)
Updated mixDeps hash in flake.nix to sha256-t8fPBGFC7wHfxgdRNEwI1k730nS7lzF750pvh0ukb7g= for the new dependencies (bandit, plug, telemetry)

The service infrastructure is now fully implemented and the Nix build works.

User (2026-02-21 21:36:48)

Do a quick change: improve parallelism while exporting org->md files. Make it configurable, by default 8.

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-21 21:36:52

<path>/home/ignaciobll/code/org-garden/lib/org_garden/export.ex</path>
<type>file</type>
<content>1: defmodule OrgGarden.Export do
2:   @moduledoc """
3:   Org-to-Markdown export via Emacs batch + ox-hugo.
4: 
5:   Provides both single-file and batch export, plus a helper to compute
6:   the expected `.md` output path for a given `.org` source file.
7:   """
8: 
9:   require Logger
10: 
11:   @doc """
12:   Export a single `.org` file to Markdown via `emacs --batch` + ox-hugo.
13: 
14:   Returns `{:ok, exit_code}` with the emacs exit code (0 = success),
15:   or `{:error, reason}` if the command could not be executed.
16:   """
17:   @spec export_file(String.t(), String.t(), String.t()) :: {:ok, non_neg_integer()} | {:error, term()}
18:   def export_file(orgfile, notes_dir, output_dir) do
19:     OrgGarden.Telemetry.span_export(orgfile, fn ->
20:       do_export_file(orgfile, notes_dir, output_dir)
21:     end)
22:   end
23: 
24:   defp do_export_file(orgfile, notes_dir, output_dir) do
25:     section =
26:       orgfile
27:       |> Path.dirname()
28:       |> Path.relative_to(notes_dir)
29: 
30:     # ox-hugo requires static/ to exist for image asset copying
31:     File.mkdir_p!(Path.join(output_dir, "static"))
32: 
33:     {output, exit_code} =
34:       System.cmd(
35:         "emacs",
36:         [
37:           "--batch",
38:           "--eval", "(require 'ox-hugo)",
39:           "--eval", """
40:           (org-cite-register-processor 'passthrough
41:             :export-citation
42:             (lambda (citation _style _backend _info)
43:               (let ((keys (mapcar (lambda (ref)
44:                                     (concat "@" (org-element-property :key ref)))
45:                                   (org-cite-get-references citation))))
46:                 (format "[cite:%s]" (string-join keys ";")))))
47:           """,
48:           "--eval", "(setq org-cite-export-processors '((t passthrough)))",
49:           "--eval", ~s[(setq org-hugo-base-dir "#{output_dir}")],
50:           "--eval", ~s[(setq org-hugo-default-section-directory "#{section}")],
51:           "--visit", orgfile,
52:           "--funcall", "org-hugo-export-to-md"
53:         ],
54:         stderr_to_stdout: true
55:       )
56: 
57:     filtered =
58:       output
59:       |> String.split("\n")
60:       |> Enum.reject(&String.match?(&1, ~r/^Loading|^ad-handle|^For information/))
61:       |> Enum.join("\n")
62: 
63:     if filtered != "", do: Logger.info("emacs: #{filtered}")
64: 
65:     if exit_code == 0 do
66:       {:ok, exit_code}
67:     else
68:       {:error, {:emacs_exit, exit_code, filtered}}
69:     end
70:   rescue
71:     e -> {:error, e}
72:   end
73: 
74:   @doc """
75:   Export all `.org` files found under `notes_dir`.
76: 
77:   Returns `{:ok, count}` where `count` is the number of successfully
78:   exported files, or `{:error, failures}` if any files failed.
79:   """
80:   @spec export_all(String.t(), String.t()) :: {:ok, non_neg_integer()} | {:error, list()}
81:   def export_all(notes_dir, output_dir) do
82:     org_files =
83:       Path.join(notes_dir, "**/*.org")
84:       |> Path.wildcard()
85: 
86:     if org_files == [] do
87:       Logger.warning("No .org files found in #{notes_dir}")
88:       {:ok, 0}
89:     else
90:       Logger.info("Exporting #{length(org_files)} org file(s) from #{notes_dir}")
91: 
92:       results =
93:         Enum.map(org_files, fn orgfile ->
94:           IO.puts("  exporting: #{orgfile}")
95:           {orgfile, export_file(orgfile, notes_dir, output_dir)}
96:         end)
97: 
98:       failures =
99:         Enum.filter(results, fn
100:           {_, {:ok, _}} -> false
101:           {_, {:error, _}} -> true
102:         end)
103: 
104:       if failures == [] do
105:         {:ok, length(results)}
106:       else
107:         {:error, failures}
108:       end
109:     end
110:   end
111: 
112:   @doc """
113:   Compute the expected `.md` path for a given `.org` file.
114: 
115:   Uses the same section-mapping logic as ox-hugo: the relative directory
116:   of the `.org` file within `notes_dir` becomes the section directory
117:   under `content_dir`.
118: 
119:   ## Examples
120: 
121:       iex> OrgGarden.Export.expected_md_path("/notes/bus/emt.org", "/notes", "/out/content")
122:       "/out/content/bus/emt.md"
123: 
124:       iex> OrgGarden.Export.expected_md_path("/notes/top-level.org", "/notes", "/out/content")
125:       "/out/content/top-level.md"
126:   """
127:   @spec expected_md_path(String.t(), String.t(), String.t()) :: String.t()
128:   def expected_md_path(orgfile, notes_dir, content_dir) do
129:     section =
130:       orgfile
131:       |> Path.dirname()
132:       |> Path.relative_to(notes_dir)
133: 
134:     basename = Path.basename(orgfile, ".org") <> ".md"
135: 
136:     case section do
137:       "." -> Path.join(content_dir, basename)
138:       _ -> Path.join([content_dir, section, basename])
139:     end
140:   end
141: end
142: 

(End of file - total 142 lines)
</content>

Tool Call [completed]: edit

Tool: edit Timestamp: 2026-02-21 21:37:07

Edit applied successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -1,6 +1,12 @@
+  @default_max_concurrency 8
+
   @doc """
   Export all `.org` files found under `notes_dir`.
 
+  Exports files in parallel for improved performance. The concurrency level
+  can be configured via the `:export_concurrency` application config or
+  the `EXPORT_CONCURRENCY` environment variable. Defaults to #{@default_max_concurrency}.
+
   Returns `{:ok, count}` where `count` is the number of successfully
   exported files, or `{:error, failures}` if any files failed.
   """
@@ -14,13 +20,21 @@
       Logger.warning("No .org files found in #{notes_dir}")
       {:ok, 0}
     else
-      Logger.info("Exporting #{length(org_files)} org file(s) from #{notes_dir}")
+      max_concurrency = get_concurrency()
+      Logger.info("Exporting #{length(org_files)} org file(s) from #{notes_dir} (concurrency: #{max_concurrency})")
 
       results =
-        Enum.map(org_files, fn orgfile ->
-          IO.puts("  exporting: #{orgfile}")
-          {orgfile, export_file(orgfile, notes_dir, output_dir)}
-        end)
+        org_files
+        |> Task.async_stream(
+          fn orgfile ->
+            Logger.info("  exporting: #{orgfile}")
+            {orgfile, export_file(orgfile, notes_dir, output_dir)}
+          end,
+          max_concurrency: max_concurrency,
+          timeout: :infinity,
+          ordered: false
+        )
+        |> Enum.map(fn {:ok, result} -> result end)
 
       failures =
         Enum.filter(results, fn
@@ -34,4 +48,8 @@
         {:error, failures}
       end
     end
+  end
+
+  defp get_concurrency do
+    Application.get_env(:org_garden, :export_concurrency, @default_max_concurrency)
   end
\ No newline at end of file

Agent (2026-02-21 21:37:09)

Now let's add the config option to runtime.exs:

Tool Call [completed]: edit

Tool: edit Timestamp: 2026-02-21 21:37:12

Edit applied successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -2,4 +2,8 @@
 config :org_garden,
   http_port: RuntimeConfig.parse_int(System.get_env("PORT"), 8080),
   ws_port: RuntimeConfig.parse_int(System.get_env("WS_PORT"), 3001),
-  health_port: RuntimeConfig.parse_int(System.get_env("HEALTH_PORT"), 9090)
\ No newline at end of file
+  health_port: RuntimeConfig.parse_int(System.get_env("HEALTH_PORT"), 9090)
+
+# Export parallelism
+config :org_garden,
+  export_concurrency: RuntimeConfig.parse_int(System.get_env("EXPORT_CONCURRENCY"), 8)
\ No newline at end of file

Agent (2026-02-21 21:37:14)

Also add to config.exs defaults:

Tool Call [completed]: edit

Tool: edit Timestamp: 2026-02-21 21:37:17

Edit applied successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -3,4 +3,5 @@
   citation_mode: :warn,
   http_port: 8080,
   ws_port: 3001,
-  health_port: 9090
\ No newline at end of file
+  health_port: 9090,
+  export_concurrency: 8
\ No newline at end of file

Agent (2026-02-21 21:37:19)

Let's verify it compiles:

Tool Call [completed]: nix develop --command mix compile --warnings-as-errors

Tool: execute Timestamp: 2026-02-21 21:37:23

warning: Git tree '/home/ignaciobll/code/org-garden' is dirty
Compiling 17 files (.ex)
Generated org_garden app

Agent (2026-02-21 21:37:25)

Now let's commit and push:

Tool Call [completed]: git add -A && git commit -m "Add parallel export with configurable concurrency (default: 8)

Use Task.async_stream for parallel org->md export. Configurable via EXPORT_CONCURRENCY env var or :export_concurrency config."

Tool: execute Timestamp: 2026-02-21 21:37:27

[main 87fd311] Add parallel export with configurable concurrency (default: 8)
 4 files changed, 9069 insertions(+), 6 deletions(-)
 create mode 100644 .agent-shell/transcripts/2026-02-21-14-47-23.md

Tool Call [completed]: git push

Tool: execute Timestamp: 2026-02-21 21:37:32

remote: . Processing 1 references        
remote: Processed 1 references in total        
To gitea.bueso.eu:ignacio.ballesteros/org-garden.git
   c54c27f..87fd311  main -> main

Agent (2026-02-21 21:37:34)

Done. The export now uses Task.async_stream for parallel processing with:

Default concurrency: 8
Configurable via EXPORT_CONCURRENCY env var or :export_concurrency config
Uses ordered: false for maximum throughput

User (2026-02-21 21:47:45)

Seems that quartz port is not properly exposed locally

Agent (2026-02-21 21:47:47)

Let me investigate the Quartz port configuration issue. Let me check the quartz.ex and how ports are passed through:

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-21 21:47:49

<path>/home/ignaciobll/code/org-garden/lib/org_garden/quartz.ex</path>
<type>file</type>
<content>1: defmodule OrgGarden.Quartz do
2:   @moduledoc """
3:   Manages Quartz Node.js process as an Erlang Port.
4: 
5:   Required environment:
6:   - QUARTZ_PATH: path to quartz repo (with node_modules)
7:   - NODE_PATH: path to node executable (default: "node")
8: 
9:   Starts Quartz in serve mode (`npx quartz build --serve`) and forwards
10:   all stdout/stderr output to the Logger with a `[quartz]` prefix.
11: 
12:   If Quartz exits, this GenServer will stop, which triggers the supervisor
13:   to restart the entire supervision tree (strategy: :one_for_all).
14:   """
15:   use GenServer
16: 
17:   require Logger
18: 
19:   alias OrgGarden.Config
20: 
21:   @shutdown_timeout 5_000
22: 
23:   defstruct [:port, :os_pid, :quartz_path, :content_dir, :http_port, :ws_port]
24: 
25:   # -------------------------------------------------------------------
26:   # Client API
27:   # -------------------------------------------------------------------
28: 
29:   @doc """
30:   Start the Quartz process as a linked GenServer.
31: 
32:   ## Options
33: 
34:     * `:content_dir` — directory where markdown files are located (required)
35:     * `:port`        — HTTP server port (default: 8080)
36:     * `:ws_port`     — WebSocket hot reload port (default: 3001)
37:   """
38:   def start_link(opts) do
39:     GenServer.start_link(__MODULE__, opts, name: __MODULE__)
40:   end
41: 
42:   @doc """
43:   Check if Quartz is running.
44:   """
45:   def running? do
46:     Process.whereis(__MODULE__) != nil
47:   end
48: 
49:   # -------------------------------------------------------------------
50:   # GenServer callbacks
51:   # -------------------------------------------------------------------
52: 
53:   @impl true
54:   def init(opts) do
55:     Process.flag(:trap_exit, true)
56: 
57:     quartz_path = Config.get!(:quartz_path)
58:     node_path = Config.get(:node_path, "node")
59: 
60:     content_dir = Keyword.fetch!(opts, :content_dir)
61:     http_port = Keyword.get(opts, :port, Config.get(:http_port, 8080))
62:     ws_port = Keyword.get(opts, :ws_port, Config.get(:ws_port, 3001))
63: 
64:     cli_path = Path.join(quartz_path, "quartz/bootstrap-cli.mjs")
65: 
66:     unless File.exists?(cli_path) do
67:       raise "Quartz CLI not found at #{cli_path}. Check QUARTZ_PATH."
68:     end
69: 
70:     args = [
71:       cli_path,
72:       "build",
73:       "--serve",
74:       "--directory",
75:       content_dir,
76:       "--port",
77:       to_string(http_port),
78:       "--wsPort",
79:       to_string(ws_port)
80:     ]
81: 
82:     Logger.info("[quartz] Starting: #{node_path} #{Enum.join(args, " ")}")
83:     Logger.info("[quartz] Working directory: #{quartz_path}")
84: 
85:     port =
86:       Port.open({:spawn_executable, node_path}, [
87:         :binary,
88:         :exit_status,
89:         :stderr_to_stdout,
90:         args: args,
91:         cd: quartz_path,
92:         env: [{~c"NODE_NO_WARNINGS", ~c"1"}]
93:       ])
94: 
95:     # Get the OS process ID for graceful shutdown
96:     {:os_pid, os_pid} = Port.info(port, :os_pid)
97: 
98:     state = %__MODULE__{
99:       port: port,
100:       os_pid: os_pid,
101:       quartz_path: quartz_path,
102:       content_dir: content_dir,
103:       http_port: http_port,
104:       ws_port: ws_port
105:     }
106: 
107:     {:ok, state}
108:   end
109: 
110:   @impl true
111:   def handle_info({port, {:data, data}}, %{port: port} = state) do
112:     data
113:     |> String.split("\n", trim: true)
114:     |> Enum.each(&Logger.info("[quartz] #{&1}"))
115: 
116:     {:noreply, state}
117:   end
118: 
119:   @impl true
120:   def handle_info({port, {:exit_status, status}}, %{port: port} = state) do
121:     Logger.error("[quartz] Process exited with status #{status}")
122:     {:stop, {:quartz_exit, status}, %{state | port: nil, os_pid: nil}}
123:   end
124: 
125:   @impl true
126:   def handle_info({:EXIT, port, reason}, %{port: port} = state) do
127:     Logger.warning("[quartz] Port terminated: #{inspect(reason)}")
128:     {:stop, {:port_exit, reason}, %{state | port: nil, os_pid: nil}}
129:   end
130: 
131:   @impl true
132:   def terminate(_reason, %{os_pid: nil}) do
133:     # Process already exited
134:     :ok
135:   end
136: 
137:   @impl true
138:   def terminate(_reason, %{port: port, os_pid: os_pid}) do
139:     Logger.info("[quartz] Shutting down gracefully...")
140: 
141:     # Send SIGTERM to the Node.js process
142:     case System.cmd("kill", ["-TERM", to_string(os_pid)], stderr_to_stdout: true) do
143:       {_, 0} ->
144:         # Wait for graceful exit
145:         wait_for_exit(port, @shutdown_timeout)
146: 
147:       {output, _} ->
148:         Logger.warning("[quartz] Failed to send SIGTERM: #{output}")
149:         force_close(port, os_pid)
150:     end
151: 
152:     :ok
153:   end
154: 
155:   # -------------------------------------------------------------------
156:   # Private functions
157:   # -------------------------------------------------------------------
158: 
159:   defp wait_for_exit(port, timeout) do
160:     receive do
161:       {^port, {:exit_status, status}} ->
162:         Logger.info("[quartz] Exited with status #{status}")
163:         :ok
164:     after
165:       timeout ->
166:         Logger.warning("[quartz] Shutdown timeout, forcing kill")
167:         {:os_pid, os_pid} = Port.info(port, :os_pid)
168:         force_close(port, os_pid)
169:     end
170:   end
171: 
172:   defp force_close(port, os_pid) do
173:     # Send SIGKILL
174:     System.cmd("kill", ["-KILL", to_string(os_pid)], stderr_to_stdout: true)
175: 
176:     # Close the port
177:     try do
178:       Port.close(port)
179:     rescue
180:       _ -> :ok
181:     end
182:   end
183: end
184: 

(End of file - total 184 lines)
</content>

Agent (2026-02-21 21:47:51)

The Quartz module looks fine. Let me check if the issue is that Quartz binds to 127.0.0.1 instead of 0.0.0.0. Let me search for how Quartz is configured:

Tool Call [completed]: nix develop --command sh -c 'cat $QUARTZ_PATH/quartz/bootstrap-cli.mjs 2>/dev/null || echo "QUARTZ_PATH not set"' | head -50

Tool: execute Timestamp: 2026-02-21 21:47:56

warning: Git tree '/home/ignaciobll/code/org-garden' is dirty
QUARTZ_PATH not set

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-21 21:47:58

<path>/home/ignaciobll/code/org-garden/quartz-config/quartz.config.ts</path>
<type>file</type>
<content>1: import { QuartzConfig } from "./quartz/cfg"
2: import * as Plugin from "./quartz/plugins"
3: 
4: /**
5:  * Quartz 4 Configuration
6:  *
7:  * See https://quartz.jzhao.xyz/configuration for more information.
8:  */
9: const config: QuartzConfig = {
10:   configuration: {
11:     pageTitle: "Quartz 4",
12:     pageTitleSuffix: "",
13:     enableSPA: true,
14:     enablePopovers: true,
15:     analytics: {
16:       provider: "plausible",
17:     },
18:     locale: "en-US",
19:     baseUrl: "quartz.jzhao.xyz",
20:     ignorePatterns: ["private", "templates", ".obsidian"],
21:     defaultDateType: "modified",
22:     theme: {
23:       fontOrigin: "googleFonts",
24:       cdnCaching: true,
25:       typography: {
26:         header: "Schibsted Grotesk",
27:         body: "Source Sans Pro",
28:         code: "IBM Plex Mono",
29:       },
30:       colors: {
31:         lightMode: {
32:           light: "#faf8f8",
33:           lightgray: "#e5e5e5",
34:           gray: "#b8b8b8",
35:           darkgray: "#4e4e4e",
36:           dark: "#2b2b2b",
37:           secondary: "#284b63",
38:           tertiary: "#84a59d",
39:           highlight: "rgba(143, 159, 169, 0.15)",
40:           textHighlight: "#fff23688",
41:         },
42:         darkMode: {
43:           light: "#161618",
44:           lightgray: "#393639",
45:           gray: "#646464",
46:           darkgray: "#d4d4d4",
47:           dark: "#ebebec",
48:           secondary: "#7b97aa",
49:           tertiary: "#84a59d",
50:           highlight: "rgba(143, 159, 169, 0.15)",
51:           textHighlight: "#b3aa0288",
52:         },
53:       },
54:     },
55:   },
56:   plugins: {
57:     transformers: [
58:       Plugin.FrontMatter({ delimiters: "+++", language: "toml" }),
59:       Plugin.CreatedModifiedDate({
60:         priority: ["frontmatter", "git", "filesystem"],
61:       }),
62:       Plugin.SyntaxHighlighting({
63:         theme: {
64:           light: "github-light",
65:           dark: "github-dark",
66:         },
67:         keepBackground: false,
68:       }),
69:       // OxHugoFlavouredMarkdown must come before GitHubFlavoredMarkdown.
70:       // Note: not compatible with ObsidianFlavoredMarkdown — use one or the other.
71:       // If ox-hugo exports TOML frontmatter, change FrontMatter to:
72:       //   Plugin.FrontMatter({ delims: "+++", language: "toml" })
73:       Plugin.OxHugoFlavouredMarkdown(),
74:       Plugin.GitHubFlavoredMarkdown(),
75:       Plugin.TableOfContents(),
76:       Plugin.CrawlLinks({ markdownLinkResolution: "shortest" }),
77:       Plugin.Description(),
78:       Plugin.Latex({ renderEngine: "katex" }),
79:     ],
80:     filters: [Plugin.RemoveDrafts()],
81:     emitters: [
82:       Plugin.AliasRedirects(),
83:       Plugin.ComponentResources(),
84:       Plugin.ContentPage(),
85:       Plugin.FolderPage(),
86:       Plugin.TagPage(),
87:       Plugin.ContentIndex({
88:         enableSiteMap: true,
89:         enableRSS: true,
90:       }),
91:       Plugin.Assets(),
92:       Plugin.Static(),
93:       Plugin.Favicon(),
94:       Plugin.NotFoundPage(),
95:       // Comment out CustomOgImages to speed up build time
96:       Plugin.CustomOgImages(),
97:     ],
98:   },
99: }
100: 
101: export default config
102: 

(End of file - total 102 lines)
</content>

Agent (2026-02-21 21:48:00)

The issue might be that Quartz by default binds to localhost (127.0.0.1). Let me check if there's a --host option we need to pass. Let me look at the Quartz CLI to see what options are available:

Tool Call [completed]: nix build .#quartz-patched && cat result/quartz/bootstrap-cli.mjs | grep -A5 -B5 "host|bind|0.0.0.0|127.0.0.1" | head -50

Tool: execute Timestamp: 2026-02-21 21:48:03

warning: Git tree '/home/ignaciobll/code/org-garden' is dirty

Tool Call [completed]:

Timestamp: 2026-02-21 21:48:13

Tool Call [completed]:

Timestamp: 2026-02-21 21:48:18

#!/usr/bin/env -S node --no-deprecation
import yargs from "yargs"
import { hideBin } from "yargs/helpers"
import {
  handleBuild,
  handleCreate,
  handleUpdate,
  handleRestore,
  handleSync,
} from "./cli/handlers.js"
import { CommonArgv, BuildArgv, CreateArgv, SyncArgv } from "./cli/args.js"
import { version } from "./cli/constants.js"

yargs(hideBin(process.argv))
  .scriptName("quartz")
  .version(version)
  .usage("$0 <cmd> [args]")
  .command("create", "Initialize Quartz", CreateArgv, async (argv) => {
    await handleCreate(argv)
  })
  .command("update", "Get the latest Quartz updates", CommonArgv, async (argv) => {
    await handleUpdate(argv)
  })
  .command(
    "restore",
    "Try to restore your content folder from the cache",
    CommonArgv,
    async (argv) => {
      await handleRestore(argv)
    },
  )
  .command("sync", "Sync your Quartz to and from GitHub.", SyncArgv, async (argv) => {
    await handleSync(argv)
  })
  .command("build", "Build Quartz into a bundle of static HTML files", BuildArgv, async (argv) => {
    await handleBuild(argv)
  })
  .showHelpOnFail(false)
  .help()
  .strict()
  .demandCommand().argv

Tool Call [completed]:

Timestamp: 2026-02-21 21:48:22

export const CommonArgv = {
  directory: {
    string: true,
    alias: ["d"],
    default: "content",
    describe: "directory to look for content files",
  },
  verbose: {
    boolean: true,
    alias: ["v"],
    default: false,
    describe: "print out extra logging information",
  },
}

export const CreateArgv = {
  ...CommonArgv,
  source: {
    string: true,
    alias: ["s"],
    describe: "source directory to copy/create symlink from",
  },
  strategy: {
    string: true,
    alias: ["X"],
    choices: ["new", "copy", "symlink"],
    describe: "strategy for content folder setup",
  },
  links: {
    string: true,
    alias: ["l"],
    choices: ["absolute", "shortest", "relative"],
    describe: "strategy to resolve links",
  },
}

export const SyncArgv = {
  ...CommonArgv,
  commit: {
    boolean: true,
    default: true,
    describe: "create a git commit for your unsaved changes",
  },
  message: {
    string: true,
    alias: ["m"],
    describe: "option to override the default Quartz commit message",
  },
  push: {
    boolean: true,
    default: true,
    describe: "push updates to your Quartz fork",
  },
  pull: {
    boolean: true,
    default: true,
    describe: "pull updates from your Quartz fork",
  },
}

export const BuildArgv = {
  ...CommonArgv,
  output: {
    string: true,
    alias: ["o"],
    default: "public",
    describe: "output folder for files",
  },
  serve: {
    boolean: true,
    default: false,
    describe: "run a local server to live-preview your Quartz",
  },
  watch: {
    boolean: true,
    default: false,
    describe: "watch for changes and rebuild automatically",
  },
  baseDir: {
    string: true,

Tool Call [completed]:

Timestamp: 2026-02-21 21:48:27

export const CommonArgv = {
  directory: {
    string: true,
    alias: ["d"],
    default: "content",
    describe: "directory to look for content files",
  },
  verbose: {
    boolean: true,
    alias: ["v"],
    default: false,
    describe: "print out extra logging information",
  },
}

export const CreateArgv = {
  ...CommonArgv,
  source: {
    string: true,
    alias: ["s"],
    describe: "source directory to copy/create symlink from",
  },
  strategy: {
    string: true,
    alias: ["X"],
    choices: ["new", "copy", "symlink"],
    describe: "strategy for content folder setup",
  },
  links: {
    string: true,
    alias: ["l"],
    choices: ["absolute", "shortest", "relative"],
    describe: "strategy to resolve links",
  },
}

export const SyncArgv = {
  ...CommonArgv,
  commit: {
    boolean: true,
    default: true,
    describe: "create a git commit for your unsaved changes",
  },
  message: {
    string: true,
    alias: ["m"],
    describe: "option to override the default Quartz commit message",
  },
  push: {
    boolean: true,
    default: true,
    describe: "push updates to your Quartz fork",
  },
  pull: {
    boolean: true,
    default: true,
    describe: "pull updates from your Quartz fork",
  },
}

export const BuildArgv = {
  ...CommonArgv,
  output: {
    string: true,
    alias: ["o"],
    default: "public",
    describe: "output folder for files",
  },
  serve: {
    boolean: true,
    default: false,
    describe: "run a local server to live-preview your Quartz",
  },
  watch: {
    boolean: true,
    default: false,
    describe: "watch for changes and rebuild automatically",
  },
  baseDir: {
    string: true,
    default: "",
    describe: "base path to serve your local server on",
  },
  port: {
    number: true,
    default: 8080,
    describe: "port to serve Quartz on",
  },
  wsPort: {
    number: true,
    default: 3001,
    describe: "port to use for WebSocket-based hot-reload notifications",
  },
  remoteDevHost: {
    string: true,
    default: "",
    describe: "A URL override for the websocket connection if you are not developing on localhost",
  },
  bundleInfo: {
    boolean: true,
    default: false,
    describe: "show detailed bundle information",
  },
  concurrency: {
    number: true,
    describe: "how many threads to use to parse notes",
  },
}

Agent (2026-02-21 21:48:31)

I see! There's no --host option directly. Let me check the handlers.js to see how the server is started:

Tool Call [failed]:

Timestamp: 2026-02-21 21:48:35

Error: The user rejected permission to use this specific tool call.

User (2026-02-21 21:49:11)

This is the log: 21:48:59.946 module=OrgGarden.Quartz [info] [quartz] Started a Quartz server listening at http://localhost:0

Agent (2026-02-21 21:49:16)

The issue is clear: Quartz is reporting localhost:0 which means the port isn't being passed correctly. Looking at the args, Quartz expects --port as a number, but we're passing it as a string. Let me check the actual command being built:

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-21 21:49:19

<path>/home/ignaciobll/code/org-garden/lib/org_garden/quartz.ex</path>
<type>file</type>
<content>70:     args = [
71:       cli_path,
72:       "build",
73:       "--serve",
74:       "--directory",
75:       content_dir,
76:       "--port",
77:       to_string(http_port),
78:       "--wsPort",
79:       to_string(ws_port)
80:     ]
81: 
82:     Logger.info("[quartz] Starting: #{node_path} #{Enum.join(args, " ")}")
83:     Logger.info("[quartz] Working directory: #{quartz_path}")
84: 
85:     port =
86:       Port.open({:spawn_executable, node_path}, [
87:         :binary,
88:         :exit_status,
89:         :stderr_to_stdout,

(File has more lines. Use 'offset' parameter to read beyond line 89)
</content>

Agent (2026-02-21 21:49:21)

The command looks correct. The issue might be that the port value itself is wrong. Let me check how the port is being retrieved in the init - it could be that Config.get(:http_port, 8080) is returning something unexpected, or that the opts aren't being passed correctly from the Supervisor.

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-21 21:49:23

<path>/home/ignaciobll/code/org-garden/lib/org_garden/supervisor.ex</path>
<type>file</type>
<content>1: defmodule OrgGarden.Supervisor do
2:   @moduledoc """
3:   Supervises development server components.
4: 
5:   Strategy: :one_for_all
6:   If either child fails, restart both to ensure consistent state.
7: 
8:   Children:
9:     1. OrgGarden.Watcher - watches .org files for changes
10:     2. OrgGarden.Quartz  - runs Quartz Node.js server
11: 
12:   ## Usage
13: 
14:       OrgGarden.Supervisor.start_link(
15:         notes_dir: "/path/to/notes",
16:         output_dir: "/path/to/output",
17:         content_dir: "/path/to/output/content",
18:         pipeline_opts: %{zotero_url: "...", ...},
19:         transforms: [OrgGarden.Transforms.Citations],
20:         port: 8080,
21:         ws_port: 3001
22:       )
23:   """
24:   use Supervisor
25: 
26:   def start_link(opts) do
27:     Supervisor.start_link(__MODULE__, opts, name: __MODULE__)
28:   end
29: 
30:   @impl true
31:   def init(opts) do
32:     children = [
33:       {OrgGarden.Watcher,
34:        Keyword.take(opts, [:notes_dir, :output_dir, :content_dir, :pipeline_opts, :transforms])},
35:       {OrgGarden.Quartz, Keyword.take(opts, [:content_dir, :port, :ws_port])}
36:     ]
37: 
38:     Supervisor.init(children, strategy: :one_for_all)
39:   end
40: end
41: 

(End of file - total 41 lines)
</content>

Agent (2026-02-21 21:49:25)

The supervisor is taking :port and :ws_port correctly. Let me trace back further to see if the Server is passing them:

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-21 21:49:26

<path>/home/ignaciobll/code/org-garden/lib/org_garden/server.ex</path>
<type>file</type>
<content>120:   @impl true
121:   def terminate(reason, state) do
122:     Logger.info("Server shutting down: #{inspect(reason)}")
123: 
124:     if state.supervisor_pid do
125:       # Stop the supervisor gracefully
126:       DynamicSupervisor.terminate_child(OrgGarden.DynamicSupervisor, state.supervisor_pid)
127:     end
128: 
129:     :ok
130:   end
131: 
132:   # -------------------------------------------------------------------
133:   # Private functions
134:   # -------------------------------------------------------------------
135: 
136:   defp run_initial_pipeline(state) do
137:     %{
138:       notes_dir: notes_dir,
139:       output_dir: output_dir,
140:       content_dir: content_dir,
141:       pipeline_opts: pipeline_opts
142:     } = state
143: 
144:     Logger.info("Running initial export pipeline...")
145: 
146:     # Wipe content directory
147:     wipe(content_dir)
148: 
149:     # Export all org files
150:     case OrgGarden.Export.export_all(notes_dir, output_dir) do
151:       {:ok, 0} ->
152:         Logger.warning("No .org files found in #{notes_dir}")
153:         :ok
154: 
155:       {:ok, count} ->
156:         Logger.info("Exported #{count} file(s)")
157: 
158:         # Run transforms
159:         {:ok, stats} = OrgGarden.run(content_dir, @transforms, pipeline_opts)

(File has more lines. Use 'offset' parameter to read beyond line 159)
</content>

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-21 21:49:29

<path>/home/ignaciobll/code/org-garden/lib/org_garden/server.ex</path>
<type>file</type>
<content>165:         # Generate index
166:         OrgGarden.Index.generate(content_dir)
167:         :ok
168: 
169:       {:error, failures} ->
170:         Logger.error("Failed to export #{length(failures)} file(s)")
171:         {:error, {:export_failed, failures}}
172:     end
173:   end
174: 
175:   defp start_supervisor(state) do
176:     %{
177:       notes_dir: notes_dir,
178:       output_dir: output_dir,
179:       content_dir: content_dir,
180:       pipeline_opts: pipeline_opts,
181:       http_port: http_port,
182:       ws_port: ws_port
183:     } = state
184: 
185:     child_spec = {
186:       OrgGarden.Supervisor,
187:       [
188:         notes_dir: notes_dir,
189:         output_dir: output_dir,
190:         content_dir: content_dir,
191:         pipeline_opts: pipeline_opts,
192:         transforms: @transforms,
193:         port: http_port,
194:         ws_port: ws_port
195:       ]
196:     }
197: 
198:     DynamicSupervisor.start_child(OrgGarden.DynamicSupervisor, child_spec)
199:   end
200: 
201:   defp wipe(content_dir) do
202:     Logger.info("Wiping #{content_dir}")
203:     File.mkdir_p!(content_dir)
204: 

(File has more lines. Use 'offset' parameter to read beyond line 204)
</content>

Agent (2026-02-21 21:49:32)

The Server is passing port: http_port correctly. Let me look at the init where http_port is set:

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-21 21:49:34

<path>/home/ignaciobll/code/org-garden/lib/org_garden/server.ex</path>
<type>file</type>
<content>60:     Process.whereis(__MODULE__) != nil
61:   end
62: 
63:   # -------------------------------------------------------------------
64:   # GenServer callbacks
65:   # -------------------------------------------------------------------
66: 
67:   @impl true
68:   def init(opts) do
69:     Process.flag(:trap_exit, true)
70: 
71:     notes_dir = Keyword.fetch!(opts, :notes_dir)
72:     output_dir = Keyword.fetch!(opts, :output_dir)
73:     content_dir = Keyword.get(opts, :content_dir, Path.join(output_dir, "content"))
74:     http_port = Keyword.get(opts, :port, Config.get(:http_port, 8080))
75:     ws_port = Keyword.get(opts, :ws_port, Config.get(:ws_port, 3001))
76: 
77:     pipeline_opts = Config.pipeline_opts()
78: 
79:     state = %{
80:       notes_dir: notes_dir,
81:       output_dir: output_dir,
82:       content_dir: content_dir,
83:       pipeline_opts: pipeline_opts,
84:       http_port: http_port,
85:       ws_port: ws_port,
86:       supervisor_pid: nil
87:     }
88: 
89:     # Run initial pipeline synchronously

(File has more lines. Use 'offset' parameter to read beyond line 89)
</content>

Agent (2026-02-21 21:49:36)

I see it now! In Server.ex line 74, it uses :port to get from opts (Keyword.get(opts, :port, ...)), but the CLI passes it as :port. That's fine. But wait - let me check where in CLI the ports are passed to Server:

Tool Call [completed]: grep

Tool: search Timestamp: 2026-02-21 21:49:39

Found 5 matches
/home/ignaciobll/code/org-garden/lib/org_garden/watcher.ex:
  Line 50:     GenServer.start_link(__MODULE__, opts, name: __MODULE__)

/home/ignaciobll/code/org-garden/lib/org_garden/quartz.ex:
  Line 39:     GenServer.start_link(__MODULE__, opts, name: __MODULE__)

/home/ignaciobll/code/org-garden/lib/org_garden/cli.ex:
  Line 78:     case OrgGarden.Server.start_link(

/home/ignaciobll/code/org-garden/lib/org_garden/server.ex:
  Line 13:       {:ok, pid} = OrgGarden.Server.start_link(
  Line 46:     GenServer.start_link(__MODULE__, opts, name: __MODULE__)

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-21 21:49:42

<path>/home/ignaciobll/code/org-garden/lib/org_garden/cli.ex</path>
<type>file</type>
<content>75: 
76:     IO.puts("==> Starting development server...")
77: 
78:     case OrgGarden.Server.start_link(
79:            notes_dir: notes_dir,
80:            output_dir: output_dir,
81:            content_dir: content_dir,
82:            port: opts[:port],
83:            ws_port: opts[:ws_port]
84:          ) do
85:       {:ok, pid} ->
86:         IO.puts("==> Server running at http://localhost:#{opts[:port] || Config.get(:http_port, 8080)}")
87:         IO.puts("==> Watching #{notes_dir} for changes (Ctrl+C to stop)")
88: 
89:         # Wait for server to exit
90:         ref = Process.monitor(pid)
91: 
92:         receive do
93:           {:DOWN, ^ref, :process, ^pid, reason} ->
94:             case reason do

(File has more lines. Use 'offset' parameter to read beyond line 94)
</content>

Agent (2026-02-21 21:49:46)

The problem is on line 82-83: port: opts[:port] and ws_port: opts[:ws_port]. When these options are not provided via CLI, opts[:port] returns nil, not the default value. Then in Server.ex:

http_port = Keyword.get(opts, :port, Config.get(:http_port, 8080))

If :port key exists but has value nil, Keyword.get returns nil, not the default! The issue is that the CLI passes nil values explicitly.

Let me fix this:

Tool Call [completed]: edit

Tool: edit Timestamp: 2026-02-21 21:49:51

Edit applied successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -1,7 +1,10 @@
-    case OrgGarden.Server.start_link(
-           notes_dir: notes_dir,
-           output_dir: output_dir,
-           content_dir: content_dir,
-           port: opts[:port],
-           ws_port: opts[:ws_port]
-         ) do
\ No newline at end of file
+    server_opts =
+      [
+        notes_dir: notes_dir,
+        output_dir: output_dir,
+        content_dir: content_dir
+      ]
+      |> maybe_put(:port, opts[:port])
+      |> maybe_put(:ws_port, opts[:ws_port])
+
+    case OrgGarden.Server.start_link(server_opts) do
\ No newline at end of file

Agent (2026-02-21 21:49:53)

Now let me add the maybe_put helper function at the end of the CLI module:

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-21 21:49:55

<path>/home/ignaciobll/code/org-garden/lib/org_garden/cli.ex</path>
<type>file</type>
<content>280:     (opts[:content_dir] || Path.join(output_dir, "content"))
281:     |> Path.expand()
282:   end
283: 
284:   # ---------------------------------------------------------------------------
285:   # Phase 1: Wipe content/
286:   # ---------------------------------------------------------------------------
287: 
288:   defp wipe(content_dir) do
289:     IO.puts("==> Wiping #{content_dir}")
290:     File.mkdir_p!(content_dir)
291: 
292:     content_dir
293:     |> File.ls!()
294:     |> Enum.reject(&(&1 == ".gitkeep"))
295:     |> Enum.each(fn entry ->
296:       Path.join(content_dir, entry) |> File.rm_rf!()
297:     end)
298:   end
299: 
300:   # ---------------------------------------------------------------------------
301:   # Phase 2: Export org files via Emacs + ox-hugo
302:   # ---------------------------------------------------------------------------
303: 
304:   defp export_all(notes_dir, output_dir) do
305:     IO.puts("==> Exporting org files from #{notes_dir}")
306: 
307:     case OrgGarden.Export.export_all(notes_dir, output_dir) do
308:       {:ok, 0} ->
309:         IO.puts("No .org files found in #{notes_dir}")

(File has more lines. Use 'offset' parameter to read beyond line 309)
</content>

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-21 21:49:57

<path>/home/ignaciobll/code/org-garden/lib/org_garden/cli.ex</path>
<type>file</type>
<content>370:         """)
371: 
372:       path ->
373:         unless File.exists?(Path.join(path, "quartz/bootstrap-cli.mjs")) do
374:           abort("Error: QUARTZ_PATH=#{path} does not contain quartz/bootstrap-cli.mjs")
375:         end
376: 
377:         path
378:     end
379:   end
380: 
381:   defp abort(message) do
382:     IO.puts(:stderr, message)
383:     System.halt(1)
384:   end
385: end
386: 

(End of file - total 386 lines)
</content>

Tool Call [completed]: edit

Tool: edit Timestamp: 2026-02-21 21:50:00

Edit applied successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -2,4 +2,7 @@
     IO.puts(:stderr, message)
     System.halt(1)
   end
+
+  defp maybe_put(keyword, _key, nil), do: keyword
+  defp maybe_put(keyword, key, value), do: Keyword.put(keyword, key, value)
 end
\ No newline at end of file

Agent (2026-02-21 21:50:02)

Now let's verify it compiles:

Tool Call [completed]: nix develop --command mix compile --warnings-as-errors

Tool: execute Timestamp: 2026-02-21 21:50:06

warning: Git tree '/home/ignaciobll/code/org-garden' is dirty
Compiling 1 file (.ex)
Generated org_garden app

Agent (2026-02-21 21:50:09)

Now let's commit and push:

Tool Call [completed]: git add -A && git commit -m "Fix Quartz port not being passed correctly

When CLI options --port/--ws-port were not provided, nil values were being explicitly passed to Server.start_link, which caused Keyword.get to return nil instead of the default. Now we only include port options in the keyword list if they have actual values."

Tool: execute Timestamp: 2026-02-21 21:50:13

[main 11ab833] Fix Quartz port not being passed correctly
 2 files changed, 1147 insertions(+), 7 deletions(-)

Tool Call [completed]: git push

Tool: execute Timestamp: 2026-02-21 21:50:17

remote: . Processing 1 references        
remote: Processed 1 references in total        
To gitea.bueso.eu:ignacio.ballesteros/org-garden.git
   87fd311..11ab833  main -> main

Agent (2026-02-21 21:50:19)

Fixed. The issue was that when CLI options --port and --ws-port weren't provided, the code was passing port: nil and ws_port: nil explicitly. Keyword.get(opts, :port, default) returns nil (not the default) when the key exists with a nil value.

Now only non-nil port values are included in the options passed to Server.start_link.

User (2026-02-22 11:44:42)

Now index.md is missing, review the pipeline and transformations

➜ org-garden git:(main) ✗

Agent (2026-02-22 11:44:46)

Let me investigate the index generation issue by reviewing the pipeline flow:

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-22 11:44:47

<path>/home/ignaciobll/code/org-garden/lib/org_garden/index.ex</path>
<type>file</type>
<content>1: defmodule OrgGarden.Index do
2:   @moduledoc """
3:   Generates a fallback `index.md` in the content directory if none was
4:   exported from an `.org` file.
5: 
6:   The generated index lists all markdown pages alphabetically with links.
7:   """
8: 
9:   @doc """
10:   Generate `content_dir/index.md` if it does not already exist.
11: 
12:   If an `index.md` was already created by ox-hugo (from an `index.org`),
13:   it is left untouched.
14:   """
15:   @spec generate(String.t()) :: :ok
16:   def generate(content_dir) do
17:     index_path = Path.join(content_dir, "index.md")
18: 
19:     unless File.exists?(index_path) do
20:       IO.puts("  generating default index.md")
21: 
22:       pages =
23:         Path.join(content_dir, "**/*.md")
24:         |> Path.wildcard()
25:         |> Enum.map(fn path ->
26:           slug = Path.relative_to(path, content_dir) |> Path.rootname()
27: 
28:           title =
29:             path
30:             |> File.read!()
31:             |> then(fn content ->
32:               case Regex.run(~r/^title\s*=\s*"(.+)"/m, content) do
33:                 [_, t] -> t
34:                 _ -> slug
35:               end
36:             end)
37: 
38:           {slug, title}
39:         end)
40:         |> Enum.sort_by(fn {_, title} -> title end)
41:         |> Enum.map(fn {slug, title} -> "- [#{title}](#{slug})" end)
42:         |> Enum.join("\n")
43: 
44:       File.write!(index_path, """
45:       ---
46:       title: Index
47:       ---
48: 
49:       #{pages}
50:       """)
51:     end
52: 
53:     :ok
54:   end
55: 
56:   @doc """
57:   Regenerate the index by removing any previously generated one first.
58: 
59:   Only removes the index if it was generated by us (contains `title: Index`).
60:   User-exported index files (from `index.org`) are left untouched.
61:   """
62:   @spec regenerate(String.t()) :: :ok
63:   def regenerate(content_dir) do
64:     index_path = Path.join(content_dir, "index.md")
65: 
66:     if File.exists?(index_path) do
67:       content = File.read!(index_path)
68: 
69:       if generated_index?(content) do
70:         File.rm!(index_path)
71:       end
72:     end
73: 
74:     generate(content_dir)
75:   end
76: 
77:   defp generated_index?(content) do
78:     # Our generated index uses "title: Index" in YAML frontmatter.
79:     # ox-hugo uses TOML frontmatter (title = "..."), so this won't
80:     # match user-exported files.
81:     String.contains?(content, "title: Index")
82:   end
83: end
84: 

(End of file - total 84 lines)
</content>

Agent (2026-02-22 11:44:49)

The index module looks fine. Let me check the server.ex to see how the pipeline is called:

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-22 11:44:51

<path>/home/ignaciobll/code/org-garden/lib/org_garden/server.ex</path>
<type>file</type>
<content>136:   defp run_initial_pipeline(state) do
137:     %{
138:       notes_dir: notes_dir,
139:       output_dir: output_dir,
140:       content_dir: content_dir,
141:       pipeline_opts: pipeline_opts
142:     } = state
143: 
144:     Logger.info("Running initial export pipeline...")
145: 
146:     # Wipe content directory
147:     wipe(content_dir)
148: 
149:     # Export all org files
150:     case OrgGarden.Export.export_all(notes_dir, output_dir) do
151:       {:ok, 0} ->
152:         Logger.warning("No .org files found in #{notes_dir}")
153:         :ok
154: 
155:       {:ok, count} ->
156:         Logger.info("Exported #{count} file(s)")
157: 
158:         # Run transforms
159:         {:ok, stats} = OrgGarden.run(content_dir, @transforms, pipeline_opts)
160: 
161:         Enum.each(stats, fn {mod, c} ->
162:           Logger.info("#{inspect(mod)}: #{c} file(s) modified")
163:         end)
164: 
165:         # Generate index
166:         OrgGarden.Index.generate(content_dir)
167:         :ok
168: 
169:       {:error, failures} ->
170:         Logger.error("Failed to export #{length(failures)} file(s)")
171:         {:error, {:export_failed, failures}}
172:     end
173:   end
174: 
175:   defp start_supervisor(state) do

(File has more lines. Use 'offset' parameter to read beyond line 175)
</content>

Agent (2026-02-22 11:44:53)

I see the issue! When there are 0 org files (line 151-153), we return :ok early without generating an index. But more importantly, let me check what happens with the parallel export - maybe it's returning early on the {:ok, 0} case incorrectly.

Let me also check the export.ex parallel code more carefully:

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-22 11:44:57

<path>/home/ignaciobll/code/org-garden/lib/org_garden/export.ex</path>
<type>file</type>
<content>74:   @default_max_concurrency 8
75: 
76:   @doc """
77:   Export all `.org` files found under `notes_dir`.
78: 
79:   Exports files in parallel for improved performance. The concurrency level
80:   can be configured via the `:export_concurrency` application config or
81:   the `EXPORT_CONCURRENCY` environment variable. Defaults to #{@default_max_concurrency}.
82: 
83:   Returns `{:ok, count}` where `count` is the number of successfully
84:   exported files, or `{:error, failures}` if any files failed.
85:   """
86:   @spec export_all(String.t(), String.t()) :: {:ok, non_neg_integer()} | {:error, list()}
87:   def export_all(notes_dir, output_dir) do
88:     org_files =
89:       Path.join(notes_dir, "**/*.org")
90:       |> Path.wildcard()
91: 
92:     if org_files == [] do
93:       Logger.warning("No .org files found in #{notes_dir}")
94:       {:ok, 0}
95:     else
96:       max_concurrency = get_concurrency()
97:       Logger.info("Exporting #{length(org_files)} org file(s) from #{notes_dir} (concurrency: #{max_concurrency})")
98: 
99:       results =
100:         org_files
101:         |> Task.async_stream(
102:           fn orgfile ->
103:             Logger.info("  exporting: #{orgfile}")
104:             {orgfile, export_file(orgfile, notes_dir, output_dir)}
105:           end,
106:           max_concurrency: max_concurrency,
107:           timeout: :infinity,
108:           ordered: false
109:         )
110:         |> Enum.map(fn {:ok, result} -> result end)
111: 
112:       failures =
113:         Enum.filter(results, fn
114:           {_, {:ok, _}} -> false
115:           {_, {:error, _}} -> true
116:         end)
117: 
118:       if failures == [] do
119:         {:ok, length(results)}
120:       else
121:         {:error, failures}
122:       end
123:     end
124:   end
125: 
126:   defp get_concurrency do
127:     Application.get_env(:org_garden, :export_concurrency, @default_max_concurrency)
128:   end
129: 
130:   @doc """
131:   Compute the expected `.md` path for a given `.org` file.
132: 
133:   Uses the same section-mapping logic as ox-hugo: the relative directory

(File has more lines. Use 'offset' parameter to read beyond line 133)
</content>

Agent (2026-02-22 11:45:00)

The export looks fine. Let me run the actual build to see what's happening. First let me check what the actual content_dir is and if index.md exists there:

Tool Call [completed]: ls -la content/ 2>/dev/null || echo "content/ doesn't exist"

Tool: execute Timestamp: 2026-02-22 11:45:02

total 8
drwxr-xr-x    2 ignaciobll users         4096 Feb 21 21:48 .
drwxr-xr-x   15 ignaciobll users         4096 Feb 21 21:48 ..

Agent (2026-02-22 11:45:06)

Content directory is empty. Let me check what notes are available:

Tool Call [completed]: ls -la notes/ 2>/dev/null || echo "notes/ doesn't exist"

Tool: execute Timestamp: 2026-02-22 11:45:07

total 20
drwxr-xr-x    5 ignaciobll users         4096 Feb 21 00:35 .
drwxr-xr-x   15 ignaciobll users         4096 Feb 21 21:48 ..
drwxr-xr-x    2 ignaciobll users         4096 Feb 21 00:35 bus
drwxr-xr-x    2 ignaciobll users         4096 Feb 21 00:35 metro
drwxr-xr-x    2 ignaciobll users         4096 Feb 21 00:35 roads

Tool Call [completed]: find notes/ -name "*.org" 2>/dev/null

Tool: execute Timestamp: 2026-02-22 11:45:10

Agent (2026-02-22 11:45:12)

There are no .org files in notes/. Let me check if there are any org files elsewhere, or if the content was previously in a different form:

Tool Call [completed]: find . -name ".org" -not -path "./.git/" 2>/dev/null | head -20

Tool: execute Timestamp: 2026-02-22 11:45:13

./README.org

Agent (2026-02-22 11:45:15)

There's only the README.org. So the actual issue is that when there are no org files to export, the index.md isn't being generated. Let me trace through the pipeline:

In server.ex:run_initial_pipeline, when export_all returns {:ok, 0}, we just return :ok without calling OrgGarden.Index.generate

Let me also check the CLI flow since you might be running the CLI directly:

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-22 11:45:19

<path>/home/ignaciobll/code/org-garden/lib/org_garden/cli.ex</path>
<type>file</type>
<content>300:   # ---------------------------------------------------------------------------
301:   # Phase 2: Export org files via Emacs + ox-hugo
302:   # ---------------------------------------------------------------------------
303: 
304:   defp export_all(notes_dir, output_dir) do
305:     IO.puts("==> Exporting org files from #{notes_dir}")
306: 
307:     case OrgGarden.Export.export_all(notes_dir, output_dir) do
308:       {:ok, 0} ->
309:         IO.puts("No .org files found in #{notes_dir}")
310:         System.halt(0)
311: 
312:       {:ok, count} ->
313:         IO.puts("  exported #{count} file(s)")
314: 
315:       {:error, failures} ->
316:         IO.puts(:stderr, "\nFailed to export #{length(failures)} file(s):")
317: 
318:         Enum.each(failures, fn {f, {:error, reason}} ->
319:           IO.puts(:stderr, "  #{f}: #{inspect(reason)}")
320:         end)
321: 
322:         System.halt(1)
323:     end
324:   end
325: 
326:   # ---------------------------------------------------------------------------
327:   # Phase 3: Markdown transformation pipeline
328:   # ---------------------------------------------------------------------------
329: 

(File has more lines. Use 'offset' parameter to read beyond line 329)
</content>

Agent (2026-02-22 11:45:22)

I see the problem! In the CLI's export_all function (line 308-310), when there are 0 org files, it calls System.halt(0) immediately - it doesn't even get to run transforms or generate the index!

But wait, you said index.md is missing. Let me check if there ARE org files being exported but the index isn't being generated. Let me trace the full serve flow:

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-22 11:45:25

<path>/home/ignaciobll/code/org-garden/lib/org_garden/cli.ex</path>
<type>file</type>
<content>118:         ]
119:       )
120: 
121:     notes_dir = extract_notes_dir(positional, "serve")
122:     output_dir = extract_output_dir(opts)
123:     content_dir = extract_content_dir(opts, output_dir)
124: 
125:     {notes_dir, output_dir, content_dir, opts}
126:   end
127: 
128:   # ---------------------------------------------------------------------------
129:   # Command: build
130:   # ---------------------------------------------------------------------------
131: 
132:   def handle_build(argv) do
133:     quartz_path = require_quartz_env()
134:     {notes_dir, output_dir, content_dir, _opts} = parse_build_args(argv)
135:     pipeline_opts = Config.pipeline_opts()
136: 
137:     # Full batch export
138:     wipe(content_dir)
139:     export_all(notes_dir, output_dir)
140:     run_pipeline(content_dir, pipeline_opts)
141:     generate_index(content_dir)
142: 
143:     node_path = Config.get(:node_path, "node")
144: 
145:     IO.puts("==> Building static site with Quartz...")
146: 
147:     {output, status} =
148:       System.cmd(
149:         node_path,
150:         [
151:           Path.join(quartz_path, "quartz/bootstrap-cli.mjs"),
152:           "build",
153:           "--directory",
154:           content_dir,
155:           "--output",
156:           Path.join(output_dir, "public")
157:         ],
158:         cd: quartz_path,
159:         stderr_to_stdout: true
160:       )
161: 
162:     IO.puts(output)
163: 
164:     if status != 0 do
165:       abort("Quartz build failed with status #{status}")
166:     end
167: 

(File has more lines. Use 'offset' parameter to read beyond line 167)
</content>

Agent (2026-02-22 11:45:27)

I see - for build command, generate_index is called (line 141), but the problem is export_all on line 139 might call System.halt(0) before we get there if no org files exist.

Let me look at where serve mode handles this:

Tool Call [completed]: read

Tool: read Timestamp: 2026-02-22 11:45:29

<path>/home/ignaciobll/code/org-garden/lib/org_garden/cli.ex</path>
<type>file</type>
<content>68:   # ---------------------------------------------------------------------------
69:   # Command: serve
70:   # ---------------------------------------------------------------------------
71: 
72:   def handle_serve(argv) do
73:     require_quartz_env()
74:     {notes_dir, output_dir, content_dir, opts} = parse_serve_args(argv)
75: 
76:     IO.puts("==> Starting development server...")
77: 
78:     server_opts =
79:       [
80:         notes_dir: notes_dir,
81:         output_dir: output_dir,
82:         content_dir: content_dir
83:       ]
84:       |> maybe_put(:port, opts[:port])
85:       |> maybe_put(:ws_port, opts[:ws_port])
86: 
87:     case OrgGarden.Server.start_link(server_opts) do
88:       {:ok, pid} ->
89:         IO.puts("==> Server running at http://localhost:#{opts[:port] || Config.get(:http_port, 8080)}")
90:         IO.puts("==> Watching #{notes_dir} for changes (Ctrl+C to stop)")
91: 
92:         # Wait for server to exit
93:         ref = Process.monitor(pid)
94: 
95:         receive do
96:           {:DOWN, ^ref, :process, ^pid, reason} ->
97:             case reason do
98:               :normal -> :ok
99:               :shutdown -> :ok
100:               {:shutdown, _} -> :ok
101:               _ -> abort("Server crashed: #{inspect(reason)}")
102:             end

(File has more lines. Use 'offset' parameter to read beyond line 102)
</content>

Agent (2026-02-22 11:45:32)

For serve, it delegates to OrgGarden.Server which calls run_initial_pipeline. The problem there is that when {:ok, 0} is returned, index is not generated.

Let me fix both issues:

In server.ex: Generate index even when there are 0 org files
In cli.ex: Don't halt immediately when 0 org files - let the pipeline continue

Tool Call [completed]: edit

Tool: edit Timestamp: 2026-02-22 11:45:39

Edit applied successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -2,6 +2,8 @@
     case OrgGarden.Export.export_all(notes_dir, output_dir) do
       {:ok, 0} ->
         Logger.warning("No .org files found in #{notes_dir}")
+        # Still generate index (will be empty or have default content)
+        OrgGarden.Index.generate(content_dir)
         :ok
 
       {:ok, count} ->

Agent (2026-02-22 11:45:41)

Now let me fix the CLI as well - it shouldn't halt immediately when there are no files. That's overly aggressive. The pipeline should still complete (even if empty):

Tool Call [completed]: edit

Tool: edit Timestamp: 2026-02-22 11:45:46

Edit applied successfully.





╭─────────╮
│ changes │
╰─────────╯

@@ -3,8 +3,7 @@
 
     case OrgGarden.Export.export_all(notes_dir, output_dir) do
       {:ok, 0} ->
-        IO.puts("No .org files found in #{notes_dir}")
-        System.halt(0)
+        IO.puts("  no .org files found")
 
       {:ok, count} ->
         IO.puts("  exported #{count} file(s)")

Agent (2026-02-22 11:45:49)

Now let's verify compilation:

Tool Call [completed]: nix develop --command mix compile --warnings-as-errors

Tool: execute Timestamp: 2026-02-22 11:45:52

warning: Git tree '/home/ignaciobll/code/org-garden' is dirty
Compiling 2 files (.ex)
Generated org_garden app

312 KiB Raw Blame History

Agent Shell Transcript

User (2026-02-21 16:40:33)

Tool Call [completed]: task

3. State Management

Current State

Issues

4. Error Recovery

Current Behavior

What's Missing

5. Graceful Shutdown

Current Implementation

Issues

6. Configuration

Current Configuration Method

What's Missing

7. Logging/Observability

Current Logging

What's Missing

8. Health Checks

Current Status

What Would Be Needed

Summary: What Exists vs What's Missing

Exists (Good Foundation)

Missing for Production Service

Recommendations for Service Conversion

Priority 1: Supervision Tree

Priority 2: Configuration

Priority 3: Observability

Priority 4: Release Support

3.2 Create Health Module

3.3 Add to Supervision Tree

Phase 4: Graceful Shutdown

4.1 Add Signal Handling

4.2 Improve Quartz Termination

4.3 Add Drain Period

Phase 5: Observability

5.1 Add Telemetry Events

5.2 Structured Logging

5.3 Replace IO.puts with Logger

Phase 6: Mix Release Support

6.1 Add Release Configuration

6.2 Create Release Scripts

6.3 Update flake.nix

Phase 7: NixOS Module

7.1 Create NixOS Module

7.2 Add to Flake Outputs

Implementation Order

Questions Before Implementation

User (2026-02-21 16:45:45)

Agent (2026-02-21 16:45:47)

Mix Release vs Escript Comparison

How CLI Works with Mix Release

Recommended Approach: Support Both Modes

Trade-off: Distribution

User (2026-02-21 16:49:13)

Agent (2026-02-21 16:49:15)

Tool Call [completed]: webfetch

lib/my_app/release_tasks.ex

In vm.args.eex

In remote.vm.args.eex

Callbacks

Callbacks

Callbacks

Tool Call [completed]: task

Pattern B: Mix Tasks (Phoenix)

Pattern C: Mix CLI Module (Mix itself)

2. Distribution Methods

Method 1: Escript (Livebook primary method)

Method 2: Mix Releases (Phoenix, Livebook production)

Method 3: Burrito (Standalone binaries)

Method 4: Bakeware (Deprecated, use Burrito)

3. Service vs CLI Distinction Patterns

Pattern 1: Command Dispatch (Livebook)

Pattern 2: Environment Configuration (Phoenix)

Pattern 3: Application Module Callback

Pattern 4: Conditional Supervision Trees (Oban)

4. Recommended Architecture for CLI + Service

CLI Entry Point

Task Behaviour

312 KiB

Raw Blame History

2. Mix Release with `eval` (Production deployments)

1.1 Refactor `application.ex`

1.2 Create `lib/org_garden/server.ex`

1.3 Update `cli.ex`

2.1 Create `config/config.exs`

2.2 Create `config/runtime.exs`

2.3 Create `lib/org_garden/config.ex`

2.4 Update modules to use `OrgGarden.Config`

3.1 Update `server.ex`

3.2 Update `quartz.ex`

3.3 Update `watcher.ex`

4.1 Add dependencies to `mix.exs`

4.2 Create `lib/org_garden/health.ex`

5.1 Create `lib/org_garden/telemetry.ex`

5.3 Replace `IO.puts` with `Logger`

6.1 Update `mix.exs`

6.2 Create `rel/env.sh.eex`

6.3 Create `rel/overlays/bin/org-garden`

7.1 Create `nix/module.nix`

7.2 Update `flake.nix`